# HG changeset patch # User iuc # Date 1614672156 0 # Node ID c1a4b5f3b432e37647ad98ec45ad012db34e7306 # Parent f7985e0479b96b43624423b003cf844f52f49b59 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 69a1a34bdcdda137182a367d063d9ff9c62cf720" diff -r f7985e0479b9 -r c1a4b5f3b432 multiqc.xml --- a/multiqc.xml Sat Nov 21 12:54:24 2020 +0000 +++ b/multiqc.xml Tue Mar 02 08:02:36 2021 +0000 @@ -53,6 +53,16 @@ @CHECK_LN_FILE@ #end for ]]> + + + + + + + + + + multiqc @@ -339,7 +349,7 @@ @LN_3_FILES@ #elif str($repeat2.type.type) == "read_duplication_pos" #for $k, $file in enumerate($repeat2.type.input) - #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.pos.DupRate.xls') + #set file_path = os.path.join($repeat_dir, 'file_' + str($k) + '.pos.DupRate.xls') ln -s '$file' '$file_path' && #end for #elif str($repeat2.type.type) == "infer_experiment" @@ -931,14 +941,16 @@ - - - - - - - - + + + + + + + + + + @@ -1019,16 +1031,18 @@ - - - - - - - - - - + + + + + + + + + + + + @@ -1231,32 +1245,32 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -1297,8 +1311,12 @@ - - + + + + + + diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/aligner_soft_report.html --- a/test-data/aligner_soft_report.html Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5608 +0,0 @@ - - - - - - - - - - - - - -MultiQC Report - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

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- v1.5 - -

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- General Stats -
- Bismark -
- - Alignment Rates -
- - Strand Alignment -
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- HiCExplorer -
- - Mapping statistics -
- - Read filtering -
- - Contact distance -
- - Read orientation -
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- Kallisto -
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- STAR -
- - Alignment Scores -
- - Gene Counts -
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- HISAT2 -
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- Tophat -
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- Bowtie 2 -
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- Cutadapt -
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If you use plots from MultiQC in a publication or presentation, please cite:

- MultiQC: Summarize analysis results for multiple tools and samples in a single report
- Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
- Bioinformatics (2016)
- doi: 10.1093/bioinformatics/btw354
- PMID: 27312411 -

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About MultiQC

This report was generated using MultiQC, version 1.5

You can see a YouTube video describing how to use MultiQC reports here: - https://youtu.be/qPbIlO_KWN0

For more information about MultiQC, including other videos and - extensive documentation, please visit http://multiqc.info

You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: - https://github.com/ewels/MultiQC

MultiQC is published in Bioinformatics:

- MultiQC: Summarize analysis results for multiple tools and samples in a single report
- Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
- Bioinformatics (2016)
- doi: 10.1093/bioinformatics/btw354
- PMID: 27312411 -

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- - -

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- A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. -

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JavaScript Disabled

MultiQC reports use JavaScript for plots and toolbox functions. It looks like - you have JavaScript disabled in your web browser. Please note that many of the report - functions will not work as intended.

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Report generated on 2018-04-23, 22:00 based on data in: - /Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_WDir - -

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General Statistics

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Sample Name	M Aligned	% Aligned	M Pairs	% Used pairs	% Mapped	Min RE dist	Max RE dist	Frag Length	M Aligned	% Aligned	M Aligned	% Aligned	% Aligned	M Aligned	% Trimmed
HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1															5.9%
HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1		83.7%						167.9bp	48.5
HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2															31.0%
HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1															7.7%
HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1		84.5%						169.4bp	59.3
HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2															32.2%
bismark_SE_report	0.2	69.7%
bowtie2_1												98.3%
bowtie2_2												98.3%
hicexplorer_hicexplorer1_1_small_test			0.1	37.3%	91.2%	303 bp	800 bp
hicexplorer_hicexplorer1_small_test			0.1	37.3%	91.2%	303 bp	800 bp
hicexplorer_hicexplorer2_small_test_rf			0.1	35.9%	91.2%	152 bp	1500 bp
hisat2_1												96.2%
hisat2_2												96.2%
star_log										89.0%	0.0
tophat_align													99.5%	0.3

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Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|	- -	Bismark	M Aligned	Total Aligned Sequences (millions)	`aligned_reads`	read_count
\|\|	- -	Kallisto	% Aligned	% processed reads that were pseudoaligned	`percent_aligned`	None
\|\|	- -	HiCExplorer	M Pairs	Total number of read pairs (millions)	`Pairs considered`	read_count
\|\|	- -	HiCExplorer	% Used pairs	% Used pairs	`Pairs used`	None
\|\|	- -	HiCExplorer	% Mapped	% Mapped	`Mapped`	None
\|\|	- -	HiCExplorer	Min RE dist	Minimum restriction site distance (bp)	`Min rest. site distance`	None
\|\|	- -	HiCExplorer	Max RE dist	Max rest. site distance (bp)	`Max rest. site distance`	None
\|\|	- -	Kallisto	Frag Length	Estimated average fragment length	`fragment_length`	None
\|\|	- -	Kallisto	M Aligned	Pseudoaligned reads (millions)	`pseudoaligned_reads`	read_count
\|\|	- -	STAR	% Aligned	% Uniquely mapped reads	`uniquely_mapped_percent`	None
\|\|	- -	STAR	M Aligned	Uniquely mapped reads (millions)	`uniquely_mapped`	read_count
\|\|	- -	Bowtie 2	% Aligned	overall alignment rate	`overall_alignment_rate`	None
\|\|	- -	Tophat	% Aligned	overall read mapping rate	`overall_aligned_percent`	None
\|\|	- -	Tophat	M Aligned	Aligned reads, not multimapped or discordant (millions)	`aligned_not_multimapped_discordant`	read_count
\|\|	- -	Cutadapt	% Trimmed	% Total Base Pairs trimmed	`percent_trimmed`	None

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Bismark

Bismark is a tool to map bisulfite converted sequence reads and determine cytosine methylation states.

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- Alignment Rates - -

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HiCExplorer

HiCExplorer addresses the common tasks of Hi-C analysis from processing to visualization.

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- Mapping statistics - - - -

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This shows how the sequenced read pairs were mapped and those filtered due to mapping problems.

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Pairs mappable, unique and high quality
- The count of reads that were considered as valid reads and were not one of the following:
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One mate unmapped
- Filtered out read because one mate was not mapped.
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One mate not unique
- Filtered out read because one mate was not unique.
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One mate low quality
- Filtered out because one mate was having a low quality.
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- Read filtering - - - -

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This figure contains the number of reads that were finally used to build the Hi-C matrix along with the reads that where filtered out.

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Dangling ends
- These are reads that start with the restriction site and constitute reads that were digested but no ligated.
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Same fragment
- These are read mates, facing inward, separated by up to 800 bp that do not have a restriction enzyme in between.
- These read pairs are not valid Hi-C pairs.
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Self circle
- Self circles are defined as pairs within 25kb with 'outward' read orientation
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Self ligation
- These are read pairs with a restriction site in between that are within 800 bp.
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- Contact distance - - - -

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This figure contains information about the distance and location of the valid pairs used.

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Long range
- Pairs with a distance greater than 20 kilobases
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Short range
- Pairs with a distance less than 20 kilobases
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Inter chromosomal
- Interchromosomal pairs.
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- Read orientation - - - -

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This figure contains information about the orientation of the read pairs.

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Inward pairs
- First mate is a forward read, second is reverse.
- ---------------> <----------------
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Outward pairs
- First mate is a reverse read, second is forward.
- ---------------> <----------------
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Left pairs
- Both are reverse reads.
- <--------------- <----------------
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Right pairs
- Both are forward reads.
- ---------------> ---------------->
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Kallisto

Kallisto is a program for quantifying abundances of transcripts from RNA-Seq data.

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STAR

STAR is an ultrafast universal RNA-seq aligner.

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- Gene Counts - -

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Statistics from results generated using --quantMode GeneCounts. The three tabs show counts for unstranded RNA-seq, counts for the 1st read strand aligned with RNA and counts for the 2nd read strand aligned with RNA.

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HISAT2

HISAT2 is a fast and sensitive alignment program for mapping NGS reads (both DNA and RNA) against a reference genome or population of reference genomes.

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Tophat

Tophat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes.

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Bowtie 2

Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences.

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This plot shows the number of reads aligning to the reference in different ways.

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There are 3 possible types of alignment: - SE Mapped uniquely: Read has only one occurence in the reference genome. - SE Multimapped: Read has multiple occurence. -* SE No aligned: Read has no occurence.

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Cutadapt

Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

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This plot shows the number of reads with certain lengths of adapter trimmed. - Obs/Exp shows the raw counts divided by the number expected due to sequencing errors. A defined peak - may be related to adapter length. See the - cutadapt documentation - for more information on how these numbers are generated.

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- - - - - - - - - - - - - - - - diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/aligner_soft_stats.tabular --- a/test-data/aligner_soft_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ -Sample Cutadapt_mqc-generalstats-cutadapt-percent_trimmed Kallisto_mqc-generalstats-kallisto-fragment_length Kallisto_mqc-generalstats-kallisto-percent_aligned Kallisto_mqc-generalstats-kallisto-pseudoaligned_reads Bismark_mqc-generalstats-bismark-aligned_reads Bismark_mqc-generalstats-bismark-percent_aligned Bowtie 2_mqc-generalstats-bowtie_2-overall_alignment_rate HiCExplorer_mqc-generalstats-hicexplorer-Pairs_considered HiCExplorer_mqc-generalstats-hicexplorer-Pairs_used HiCExplorer_mqc-generalstats-hicexplorer-Mapped HiCExplorer_mqc-generalstats-hicexplorer-Min_rest_site_distance HiCExplorer_mqc-generalstats-hicexplorer-Max_rest_site_distance HISAT2_mqc-generalstats-hisat2-overall_alignment_rate STAR_mqc-generalstats-star-uniquely_mapped_percent STAR_mqc-generalstats-star-uniquely_mapped Tophat_mqc-generalstats-tophat-overall_aligned_percent Tophat_mqc-generalstats-tophat-aligned_not_multimapped_discordant MACS2_mqc-generalstats-macs2-d MACS2_mqc-generalstats-macs2-treatment_redundant_rate MACS2_mqc-generalstats-macs2-control_redundant_rate -HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1 5.880883098970165 -HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 167.866 83.65114569077758 48531088.0 -HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2 31.038195169381073 -HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1 7.7267901650356645 -HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 169.418 84.50278473550448 59280920.0 -HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2 32.18485266309055 -bismark_txt_SE_report 220558.0 69.71079996207212 -bowtie2_1_txt 98.33 -bowtie2_2_txt 98.31 -hicexplorer_3_hicexplorer1_log_1_small_test 99983.0 0.3732734564876029 0.08778492343698428 303.0 800.0 -hicexplorer_3_hicexplorer1_log_small_test 99983.0 0.3732734564876029 0.08778492343698428 303.0 800.0 -hicexplorer_3_hicexplorer2_log_small_test_rf 99983.0 0.35940109818669175 0.08778492343698428 152.0 1500.0 -hisat2_1_txt 96.15 -hisat2_2_txt 96.15 -star_log_txt 89.0 89.0 -tophat_txtalign 99.5 307733.0 -treat1 254.0 0.0 0.0 -treat2 254.0 0.0 0.0 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/bamtools_stats.tabular --- a/test-data/bamtools_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample total_reads forward_strand mapped_reads both_mapped_pct read_1 mapped_reads_pct failed_qc_pct forward_strand_pct reverse_strand paired_end paired_end_pct duplicates_pct singletons read_2 both_mapped failed_qc reverse_strand_pct singletons_pct duplicates -bamtools 339957930.0 181666967.0 316585701.0 92.3705 169978965.0 93.125 0.0 53.4381 158290963.0 339957930.0 100.0 0.0 2564985.0 169978965.0 314020716.0 0.0 46.5619 0.754501 0.0 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/bcftools_stats.tabular --- a/test-data/bcftools_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample number_of_samples tstv substitution_type_C>T substitution_type_A>C substitution_type_T>C number_of_multiallelic_sites tv_1st_ALT substitution_type_A>T substitution_type_A>G substitution_type_T>A ts number_of_multiallelic_SNP_sites substitution_type_C>A substitution_type_G>A substitution_type_G>C number_of_MNPs tstv_1st_ALT number_of_records number_of_others tv number_of_SNPs number_of_indels number_of_no-ALTs substitution_type_T>G substitution_type_C>G substitution_type_G>T ts_1st_ALT -Test1 1.0 1.97 762114.0 190164.0 721436.0 0.0 1505704.0 166827.0 721395.0 166222.0 2968539.0 0.0 196831.0 763594.0 197866.0 72330.0 1.97 5522770.0 73262.0 1505704.0 4474244.0 902934.0 0.0 189578.0 197211.0 201005.0 2968539.0 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/bismark_stats.tabular --- a/test-data/bismark_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample aligned_reads ambig_reads discarded_reads meth_chg meth_chh meth_cpg no_alignments percent_aligned percent_chg_meth percent_chh_meth percent_cpg_meth strand_ctob strand_ctot strand_ob strand_ot total_c total_reads unmeth_chg unmeth_chh unmeth_cpg -bismark_SE_report 220558.0 1904.0 0.0 1358074.0 3449120.0 465068.0 93928.0 69.71079996207212 99.8 99.7 98.6 0.0 0.0 112206.0 108352.0 5291918.0 316390.0 2988.0 10269.0 6399.0 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/bowtie2_stats.tabular --- a/test-data/bowtie2_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -Sample unpaired_total total_reads unpaired_aligned_one unpaired_aligned_none overall_alignment_rate unpaired_aligned_multi -bowtie2_1 21040602 21040602 13299463 351563 98.33 7389576 -bowtie2_2 16199126 16199126 10087714 274008 98.31 5837404 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/busco_stats.tabular --- a/test-data/busco_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample fragmented complete_single_copy total complete missing lineage_dataset complete_duplicated -busco 5.0 255.0 290.0 257.0 28.0 fungi_odb9 2.0 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/cc_ko15.bpc.embedded.tab --- a/test-data/cc_ko15.bpc.embedded.tab Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1289 +0,0 @@ -# file_format: 'tsv' -# section_name: 'BPC' -# title: 'Base peak chromatogram' -# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)' -# plot_type: 'linegraph' -# pconfig: -# id: 'bpc_lineplot' -# title: 'Base peak chromatogram' -# ylab: 'Base Peak Intensity' -# xlab: 'Retention Time' -Retention Time Base Peak Intensity -2502.98928676082 43888 -2504.55428676082 43960 -2506.11928676082 43392 -2507.68428676082 42632 -2509.24928676082 42200 -2510.81428676082 42288 -2512.37928676082 42664 -2513.94428676082 42480 -2515.50928676082 42320 -2517.07428676082 42528 -2518.63928676082 43376 -2520.20428676082 44240 -2521.76928676082 44696 -2523.33328676082 44560 -2524.89828676082 44112 -2526.46328676082 43936 -2528.02828676082 43736 -2529.59328676082 42912 -2531.15828676082 42360 -2532.72328676082 43128 -2534.28828676082 43880 -2535.85328676082 44104 -2537.41828676082 44256 -2538.98328676082 44664 -2540.54828676082 44600 -2542.11328676082 44224 -2543.67828676082 44120 -2545.24328676082 44328 -2546.80828676082 44536 -2548.37328676082 44872 -2549.93828676082 44592 -2551.50328676082 43600 -2553.06828676082 42872 -2554.63328676082 43528 -2556.19728676082 44072 -2557.76228676082 43360 -2559.32728676082 41632 -2560.89228676082 40752 -2562.45728676082 40472 -2564.02228676082 39792 -2565.58728676082 39096 -2567.15228676082 39696 -2568.71728676082 41152 -2570.28228676082 41896 -2571.84728676082 41568 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-4478.56615089905 4920 -4480.13115089905 4294 -4481.69615089905 3437 -4483.26115089905 3096 -4484.82615089905 3312 -4486.39115089905 3426 -4487.95615089905 3085 -4489.52115089905 2750 -4491.08615089905 2696 -4492.65115089905 2920 -4494.21615089905 3119 -4495.78115089905 3322 -4497.34615089905 3463 -4498.91115089905 3313 -4500.47615089905 3184 -4502.04115089905 3217 -4503.60615089905 3240 -4505.17115089905 3288 -4506.73615089905 3582 -4508.30115089905 3963 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/cutadapt_stats.tabular --- a/test-data/cutadapt_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample r_trimmed percent_trimmed too_long too_short r_processed bp_processed bp_trimmed -dataset_33 68795 10.776820436239396 0 0 316390 31955390 3443775 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/fastp_stats.tabular --- a/test-data/fastp_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -Sample command -R1_fq fastp --thread 1 --report_title fastp report for R1_fq.fastq -i R1_fq.fastq -o first.fastq -U --umi_loc read1 --umi_len 8 -bwa-mem-fastq1_fq fastp --thread 1 --report_title fastp report for bwa-mem-fastq1_fq.fastq -i bwa-mem-fastq1_fq.fastq -o first.fastq -I bwa-mem-fastq2_fq.fastq -O second.fastq diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/fastqc_stats.tabular --- a/test-data/fastqc_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -Sample Filename File type Total Sequences sequence_duplication_levels overrepresented_sequences per_base_sequence_content per_base_sequence_quality per_base_n_content sequence_length_distribution %GC Encoding total_deduplicated_percentage per_sequence_quality_scores per_tile_sequence_quality Sequence length avg_sequence_length per_sequence_gc_content basic_statistics adapter_content Sequences flagged as poor quality kmer_content -poulet5_1 poulet5_1 Conventional base calls 267849.0 warn pass fail warn pass pass 48.0 Sanger / Illumina 1.9 63.69408840068983 warn pass 101.0 101.0 pass pass pass 0.0 warn -poulet5_2 poulet5_2 Conventional base calls 267849.0 warn pass fail warn pass pass 48.0 Sanger / Illumina 1.9 63.826611251945884 warn pass 101.0 101.0 pass pass pass 0.0 warn diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/featureCounts_stats.tabular --- a/test-data/featureCounts_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -Sample Unassigned_MappingQuality Unassigned_Nonjunction Unassigned_Unmapped Unassigned_Chimera percent_assigned Unassigned_NoFeatures Unassigned_Secondary Assigned Unassigned_FragmentLength Unassigned_Duplicate Unassigned_MultiMapping Unassigned_Ambiguity Total -70: TopHat on data 1, data 4, and data 3: accepted_hits 0 0 0 0 70.82267755353567 111117 0 321797 0 0 19123 2333 454370 -75: TopHat on data 1, data 6, and data 5: accepted_hits 0 0 0 0 69.58585803304067 165786 0 445012 0 0 25293 3424 639515 -80: TopHat on data 1, data 8, and data 7: accepted_hits 0 0 0 0 71.76957768385707 129664 0 394981 0 0 22580 3121 550346 -85: TopHat on data 1, data 10, and data 9: accepted_hits 0 0 0 0 72.02454351337069 146327 0 437485 0 0 19907 3692 607411 -90: TopHat on data 1, data 12, and data 11: accepted_hits 0 0 0 0 71.33130826437625 132063 0 388170 0 0 21164 2782 544179 -95: TopHat on data 1, data 14, and data 13: accepted_hits 0 0 0 0 70.72517103678439 160805 0 453929 0 0 23533 3554 641821 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/flexbar_stats.tabular --- a/test-data/flexbar_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample remaining_reads removed_bases finally_skipped_short_reads skipped_due_to_uncalled_bases short_prior_to_adapter_removal processed_reads processed_bases removed_bases_pct discarded_reads_overall remaining_bases -result_right 10 191 3 0 0 13 422 45.26066350710901 3 231 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/gatk_varianteval_stats.tabular --- a/test-data/gatk_varianteval_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample mnps symbolic complex nocalls deletions known_titv titv_reference novel_titv snps mixed insertions -gatk_varianteval 0 0 0 1330372586 0 0.0 none 2.2 19199310 0 0 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/hicup_deduplicator.txt --- a/test-data/hicup_deduplicator.txt Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -File Read_pairs_processed Unique_di-tags Cis_<10kbp_of_uniques Cis_>10kbp_of_uniques Trans_of_uniques -Sample-1.A007.C8DRAANXX.s_2.r_1_2.filt.bam 7029431 6978457 876396 4591811 1510250 -Sample-1.A002.C8DRAANXX.s_2.r_1_2.filt.bam 8935388 8864466 1159324 5742469 1962673 -Sample-1.A005.C8DRAANXX.s_2.r_1_2.filt.bam 11314841 11219537 1495237 7243835 2480465 -Sample-1.A019.C8DRAANXX.s_2.r_1_2.filt.bam 11766363 11658185 1811982 7779338 2066865 -Sample-1.A012.C8DRAANXX.s_2.r_1_2.filt.bam 11705308 11609411 1261011 7003201 3345199 -Sample-1.A006.C8DRAANXX.s_2.r_1_2.filt.bam 13106391 12998003 2043926 8107586 2846491 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/hicup_filter.txt --- a/test-data/hicup_filter.txt Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7 +0,0 @@ -File Total_pairs Valid_pairs Cis_<10kbp Cis_>10kbp Trans Invalid_pairs Same_circularised Same_dangling_ends Same_internal Re-ligation Contiguous_sequence Wrong_size -Sample-1.A002.C8DRAANXX.s_2.r_1_2.pair.bam 14383198 8935388 1169666 5787588 1978134 5447810 136087 530246 2442480 834795 48328 1455874 -Sample-1.A007.C8DRAANXX.s_2.r_1_2.pair.bam 14621513 7029431 882929 4625450 1521052 7592082 157241 452563 4031859 771757 37367 2141295 -Sample-1.A005.C8DRAANXX.s_2.r_1_2.pair.bam 15245021 11314841 1509270 7304795 2500776 3930180 187236 298334 1580105 924315 59919 880271 -Sample-1.A019.C8DRAANXX.s_2.r_1_2.pair.bam 16053923 11766363 1830414 7850293 2085656 4287560 223187 305385 1541376 1070842 72067 1074703 -Sample-1.A006.C8DRAANXX.s_2.r_1_2.pair.bam 18473566 13106391 2063334 8173491 2869566 5367175 220527 408217 2075370 961388 65086 1636587 -Sample-1.A012.C8DRAANXX.s_2.r_1_2.pair.bam 19070455 11705308 1272882 7060212 3372214 7365147 163868 663463 3810160 976378 55368 1695910 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/hicup_mapper.txt --- a/test-data/hicup_mapper.txt Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -File Total_reads_processed Reads_too_short_to_map %Reads_too_short_to_map Unique_alignments %Unique_alignments Multiple_alignments %Multiple_alignments Failed_to_align %failed_to_align Paired %Paired -Sample-1.A006.C8DRAANXX.s_2.r_1.trunc.fastq.gz 34760244 579570 1.7 25926210 74.6 5230796 15.0 3023668 8.7 18473566 53.1 -Sample-1.A006.C8DRAANXX.s_2.r_2.trunc.fastq.gz 34760244 539500 1.6 25637256 73.8 5121683 14.7 3461805 10.0 18473566 53.1 -Sample-1.A005.C8DRAANXX.s_2.r_1.trunc.fastq.gz 26780491 431302 1.6 20379141 76.1 4263954 15.9 1706094 6.4 15245021 56.9 -Sample-1.A005.C8DRAANXX.s_2.r_2.trunc.fastq.gz 26780491 407260 1.5 20071745 74.9 4167422 15.6 2134064 8.0 15245021 56.9 -Sample-1.A012.C8DRAANXX.s_2.r_1.trunc.fastq.gz 35472550 526747 1.5 26504291 74.7 5362349 15.1 3079163 8.7 19070455 53.8 -Sample-1.A012.C8DRAANXX.s_2.r_2.trunc.fastq.gz 35472550 494718 1.4 26142222 73.7 5264577 14.8 3571033 10.1 19070455 53.8 -Sample-1.A002.C8DRAANXX.s_2.r_1.trunc.fastq.gz 28754600 751623 2.6 21072845 73.3 4475271 15.6 2454861 8.5 14383198 50.0 -Sample-1.A002.C8DRAANXX.s_2.r_2.trunc.fastq.gz 28754600 698375 2.4 20505141 71.3 4336149 15.1 3214935 11.2 14383198 50.0 -Sample-1.A007.C8DRAANXX.s_2.r_1.trunc.fastq.gz 31000250 368533 1.2 22327487 72.0 4263821 13.8 4040409 13.0 14621513 47.2 -Sample-1.A007.C8DRAANXX.s_2.r_2.trunc.fastq.gz 31000250 338254 1.1 21828226 70.4 4140992 13.4 4692778 15.1 14621513 47.2 -Sample-1.A019.C8DRAANXX.s_2.r_1.trunc.fastq.gz 28583413 519100 1.8 21667602 75.8 4404215 15.4 1992496 7.0 16053923 56.2 -Sample-1.A019.C8DRAANXX.s_2.r_2.trunc.fastq.gz 28583413 488517 1.7 21491634 75.2 4342639 15.2 2260623 7.9 16053923 56.2 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/hicup_truncater.txt --- a/test-data/hicup_truncater.txt Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -File Total_Reads_Processed Truncated %Truncated Not_truncated %Not_truncated Average_length_truncated_sequence -Sample-1.A002.C8DRAANXX.s_2.r_1.fq 28754600 7548969 26.25 21205631 73.75 58.69 -Sample-1.A002.C8DRAANXX.s_2.r_2.fq 28754600 7446167 25.90 21308433 74.10 59.65 -Sample-1.A006.C8DRAANXX.s_2.r_2.fq 34760244 10523907 30.28 24236337 69.72 66.68 -Sample-1.A012.C8DRAANXX.s_2.r_2.fq 35472550 9050477 25.51 26422073 74.49 66.30 -Sample-1.A006.C8DRAANXX.s_2.r_1.fq 34760244 10420308 29.98 24339936 70.02 65.67 -Sample-1.A012.C8DRAANXX.s_2.r_1.fq 35472550 8999621 25.37 26472929 74.63 65.39 -Sample-1.A005.C8DRAANXX.s_2.r_2.fq 26780491 8436781 31.50 18343710 68.50 67.02 -Sample-1.A005.C8DRAANXX.s_2.r_1.fq 26780491 8361813 31.22 18418678 68.78 66.22 -Sample-1.A019.C8DRAANXX.s_2.r_2.fq 28583413 9321837 32.61 19261576 67.39 66.38 -Sample-1.A019.C8DRAANXX.s_2.r_1.fq 28583413 9151107 32.02 19432306 67.98 65.11 -Sample-1.A007.C8DRAANXX.s_2.r_1.fq 31000250 6212988 20.04 24787262 79.96 65.01 -Sample-1.A007.C8DRAANXX.s_2.r_2.fq 31000250 6187239 19.96 24813011 80.04 65.94 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/hisat2_stats.tabular --- a/test-data/hisat2_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -Sample unpaired_total overall_alignment_rate unpaired_aligned_one unpaired_aligned_none unpaired_aligned_multi -hisat2_1 99978 96.15 86176 3849 9953 -hisat2_2 99978 96.15 86176 3849 9953 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/htseq_stats.tabular --- a/test-data/htseq_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample alignment_not_unique assigned total_count not_aligned percent_assigned no_feature too_low_aQual ambiguous -htseq 0 0 1355 1336 0.0 19 0 0 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/kallisto_stats.tabular --- a/test-data/kallisto_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -Sample percent_aligned total_reads not_pseudoaligned_reads pseudoaligned_reads fragment_length -HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 83.65114569077758 58016047.0 9484959.0 48531088.0 167.866 -HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 84.50278473550448 70152623.0 10871703.0 59280920.0 169.418 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/macs_stats.tabular --- a/test-data/macs_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -Sample fragment_size treatment_fragments_total treatment_fragments_after_filtering treatment_max_duplicates treatment_redundant_rate control_fragments_total control_fragments_after_filtering control_max_duplicates control_redundant_rate d -treat1 100.0 199977.0 199583.0 1.0 0.0 199978.0 199867.0 1.0 0.0 254.0 -treat2 100.0 100000.0 99795.0 1.0 0.0 199978.0 199867.0 1.0 0.0 254.0 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/picard_AlignmentSummaryMetrics_stats.tabular --- a/test-data/picard_AlignmentSummaryMetrics_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample CATEGORY PF_HQ_ALIGNED_Q20_BASES PF_HQ_ALIGNED_BASES READ_GROUP PF_HQ_ALIGNED_READS PF_MISMATCH_RATE LIBRARY PCT_READS_ALIGNED_IN_PAIRS MEAN_READ_LENGTH PF_HQ_MEDIAN_MISMATCHES SAMPLE PF_HQ_ERROR_RATE READS_ALIGNED_IN_PAIRS PF_READS TOTAL_READS PF_INDEL_RATE PCT_ADAPTER STRAND_BALANCE PCT_PF_READS PF_READS_ALIGNED PF_NOISE_READS BAD_CYCLES PCT_CHIMERAS PF_ALIGNED_BASES PCT_PF_READS_ALIGNED -D11_H4K16ac_Rep1_R1_fastq_gz UNPAIRED 802235299.0 843872901.0 11288718.0 0.011597 0.0 74.733459 0.0 0.006165 0.0 16199126.0 16199126.0 0.000848 1.4e-05 0.494061 1.0 15925118.0 112.0 0.0 0.0 1189439864.0 0.983085 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/picard_RnaSeqMetrics_stats.tabular --- a/test-data/picard_RnaSeqMetrics_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample READ_GROUP INCORRECT_STRAND_READS PF_NOT_ALIGNED_BASES PCT_CODING_BASES PCT_USABLE_BASES MEDIAN_5PRIME_TO_3PRIME_BIAS PCT_CORRECT_STRAND_READS RIBOSOMAL_BASES LIBRARY IGNORED_READS PCT_INTRONIC_BASES INTRONIC_BASES PCT_INTERGENIC_BASES PCT_RIBOSOMAL_BASES MEDIAN_3PRIME_BIAS SAMPLE MEDIAN_CV_COVERAGE UTR_BASES INTERGENIC_BASES CORRECT_STRAND_READS PCT_UTR_BASES CODING_BASES MEDIAN_5PRIME_BIAS PCT_MRNA_BASES PF_BASES PF_ALIGNED_BASES -picard_CollectRnaSeqMetrics_bam 0.0 158.0 0.0 79.36569999999999 1.402829 0.0 0.0 0.0 0.0 20.3769 0.235755 0.91593 38786.0 9926.0 0.0 79.62310000000001 0.0 0.430026 79.62310000000001 48870.0 48712.0 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/picard_baseContent_stats.tabular --- a/test-data/picard_baseContent_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample mean_pct_t mean_pct_g sum_pct_c sum_pct_t mean_pct_c mean_pct_a sum_pct_n cycle_count sum_pct_g sum_pct_a -D11_H4K16ac_Rep1_R1_fastq_gz 28.154420613333333 21.205210626666666 1545.9380260000005 2111.581546 20.61250701333334 30.02120486666666 0.49925800000000015 75 1590.390797 2251.5903649999996 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/picard_dups_stats.tabular --- a/test-data/picard_dups_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample READ_PAIR_DUPLICATES UNPAIRED_READS_EXAMINED LIBRARY READ_PAIRS_EXAMINED UNPAIRED_READ_DUPLICATES UNMAPPED_READS ESTIMATED_LIBRARY_SIZE PERCENT_DUPLICATION READ_PAIR_OPTICAL_DUPLICATES -dataset_114 629.0 2900.0 Unknown Library 313405.0 2257.0 0.0 77973949.0 0.005582 0.0 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/picard_insertSize_stats.tabular --- a/test-data/picard_insertSize_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample SAMPLE_NAME MEDIAN_INSERT_SIZE MEDIAN_ABSOLUTE_DEVIATION MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS PAIR_ORIENTATION WIDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT WIDTH_OF_70_PERCENT WIDTH_OF_80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_99_PERCENT SAMPLE LIBRARY READ_GROUP -dataset_197_FR dataset_197 194.0 63.0 100.0 5331452.0 271.809759 196.076488 311788.0 FR 25.0 47.0 69.0 91.0 127.0 343.0 941.0 1515.0 2585.0 16663.0 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/post_aligner_soft_report.html --- a/test-data/post_aligner_soft_report.html Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,7363 +0,0 @@ - - - - - - - - - - - - - -MultiQC Report - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

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- MultiQC: Summarize analysis results for multiple tools and samples in a single report
- Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
- Bioinformatics (2016)
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About MultiQC

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MultiQC is published in Bioinformatics:

- MultiQC: Summarize analysis results for multiple tools and samples in a single report
- Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
- Bioinformatics (2016)
- doi: 10.1093/bioinformatics/btw354
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General Statistics

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Sample Name	M Reads Mapped	N50 (Kbp)	Length (Mbp)	Change rate	Ts/Tv	M Variants	TiTV ratio (known)	TiTV ratio (novel)	% Assigned	M Assigned	Vars	SNP	Indel	Ts/Tv	MNP	M Assigned	% rRNA	% mRNA	% Aligned	Insert Size	Mean Insert Size	% Dups	Organism	Contigs	Bases	CDS	% Dups	Error rate	M Non-Primary	M Reads Mapped	% Mapped	M Total seqs	% Duplicates	% Mapped
14892_1#15		115.1Kbp	18.4Mbp
70: TopHat on data 1, data 4, and data 3: accepted_hits									70.8%							0.3
75: TopHat on data 1, data 6, and data 5: accepted_hits									69.6%							0.4
80: TopHat on data 1, data 8, and data 7: accepted_hits									71.8%							0.4
85: TopHat on data 1, data 10, and data 9: accepted_hits									72.0%							0.4
90: TopHat on data 1, data 12, and data 11: accepted_hits									71.3%							0.4
95: TopHat on data 1, data 14, and data 13: accepted_hits									70.7%							0.5
D11_H4K16ac_Rep1_R1_fastq_gz																			98%
Sample1																							Helicobacter pylori	30.0	1629978	1548
Sample2																							Escherichia coli	52.0	162997532523	1548
Test1											5522770	4474244	902934	1.97	72330
bamtools																																	0.0%	93.1%
dataset_114																						0.6%
dataset_197																				176 bp	272 bp
gatk_varianteval							0.0	2.2
htseq									0.0%	0.0
picard_CollectRnaSeqMetrics_bam																	%	79.6%
samtools_flagstat	20.7
samtools_stats																												0.42%	0.0	0.6	100.0%	0.6
snpeff				3190	0.000	0.97
virtual-normal																											1.3%

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|	- -	Samtools Flagstat	M Reads Mapped	Reads Mapped in the bam file (millions)	`mapped_passed`	read_count
\|\|	- -	QUAST	N50 (Kbp)	N50 is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the assembly (kilo base pairs)	`N50`	None
\|\|	- -	QUAST	Length (Mbp)	The total number of bases in the assembly (mega base pairs).	`Total length`	None
\|\|	- -	SnpEff	Change rate	Change rate	`Change_rate`	None
\|\|	- -	SnpEff	Ts/Tv	Transitions / Transversions ratio	`Ts_Tv_ratio`	None
\|\|	- -	SnpEff	M Variants	Number of variants before filter (millions)	`Number_of_variants_before_filter`	None
\|\|	- -	GATK VariantEval	TiTV ratio (known)	TiTV ratio from variants found in 'none'	`known_titv`	titv_ratio
\|\|	- -	GATK VariantEval	TiTV ratio (novel)	TiTV ratio from variants NOT found in 'none'	`novel_titv`	titv_ratio
\|\|	- -	featureCounts	% Assigned	% Assigned reads	`percent_assigned`	None
\|\|	- -	HTSeq Count	M Assigned	Assigned Reads (millions)	`assigned`	read_count
\|\|	- -	Bcftools Stats	Vars	Variations total	`number_of_records`	None
\|\|	- -	Bcftools Stats	SNP	Variation SNPs	`number_of_SNPs`	None
\|\|	- -	Bcftools Stats	Indel	Variation Insertions/Deletions	`number_of_indels`	None
\|\|	- -	Bcftools Stats	Ts/Tv	Variant SNP transition / transversion ratio	`tstv`	None
\|\|	- -	Bcftools Stats	MNP	Variation multinucleotide polymorphisms	`number_of_MNPs`	None
\|\|	- -	featureCounts	M Assigned	Assigned reads (millions)	`Assigned`	read_count
\|\|	- -	Picard	% rRNA	Percent of aligned bases overlapping ribosomal RNA regions	`PCT_RIBOSOMAL_BASES`	None
\|\|	- -	Picard	% mRNA	Percent of aligned bases overlapping UTRs and coding regions of mRNA transcripts	`PCT_MRNA_BASES`	None
\|\|	- -	Picard	% Aligned	Percent of aligned reads	`PCT_PF_READS_ALIGNED`	None
\|\|	- -	Picard	Insert Size	Median Insert Size, all read orientations (bp)	`summed_median`	None
\|\|	- -	Picard	Mean Insert Size	Mean Insert Size, all read orientations (bp)	`summed_mean`	None
\|\|	- -	Picard	% Dups	MarkDuplicates - Percent Duplication	`PERCENT_DUPLICATION`	None
\|\|	- -	Prokka	Organism	Organism	`organism`	None
\|\|	- -	Prokka	Contigs	Number of contigs	`contigs`	None
\|\|	- -	Prokka	Bases	Number of bases	`bases`	None
\|\|	- -	Prokka	CDS	Number of CDS	`CDS`	None
\|\|	- -	Samblaster	% Dups	Percent Duplication	`pct_dups`	None
\|\|	- -	Samtools Stats	Error rate	Error rate: mismatches (NM) / bases mapped (CIGAR)	`error_rate`	None
\|\|	- -	Samtools Stats	M Non-Primary	Non-primary alignments (millions)	`non-primary_alignments`	read_count
\|\|	- -	Samtools Stats	M Reads Mapped	Reads Mapped in the bam file (millions)	`reads_mapped`	read_count
\|\|	- -	Samtools Stats	% Mapped	% Mapped Reads	`reads_mapped_percent`	None
\|\|	- -	Samtools Stats	M Total seqs	Total sequences in the bam file (millions)	`raw_total_sequences`	read_count
\|\|	- -	Bamtools	% Duplicates	% Duplicate Reads	`duplicates_pct`	None
\|\|	- -	Bamtools	% Mapped	% Mapped Reads	`mapped_reads_pct`	None

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QUAST

QUAST is a quality assessment tool for genome assemblies, written by the Center for Algorithmic Biotechnology.

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- Assembly Statistics - -

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- - - - - - - - - Showing ¹/₁ rows and ¹²/₁₂ columns. - -

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Sample Name	N50 (Kbp)	N75 (Kbp)	L50 (K)	L75 (K)	Largest contig (Kbp)	Length (Mbp)	Misassemblies	Mismatches/100kbp	Indels/100kbp	Genes	Genes (Partial)	Genome Fraction
14892_1#15	115.1Kbp	62.3Kbp	0.0K	100.0K	435.5Kbp	18.4Mbp	107.0	262.21	33.75	7280	968	95.5%

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|	- -	QUAST	N50 (Kbp)	N50 is the contig length such that using longer or equal length contigs produces half (50%) of the bases of the assembly.	`N50`	None
\|\|	- -	QUAST	N75 (Kbp)	N75 is the contig length such that using longer or equal length contigs produces 75% of the bases of the assembly	`N75`	None
\|\|	- -	QUAST	L50 (K)	L50 is the number of contigs larger than N50, i.e. the minimum number of contigs comprising 50% of the total assembly length.	`L50`	None
\|\|	- -	QUAST	L75 (K)	L75 is the number of contigs larger than N75, i.e. the minimum number of contigs comprising 75% of the total assembly length.	`L75`	None
\|\|	- -	QUAST	Largest contig (Kbp)	The size of the largest contig of the assembly	`Largest contig`	None
\|\|	- -	QUAST	Length (Mbp)	The total number of bases in the assembly.	`Total length`	None
\|\|	- -	QUAST	Misassemblies	The number of positions in the assembled contigs where the left flanking sequence aligns over 1 kbp away from the right flanking sequence on the reference (relocation) or they overlap on more than 1 kbp (relocation) or flanking sequences align on different strands (inversion) or different chromosomes (translocation).	`# misassemblies`	None
\|\|	- -	QUAST	Mismatches/100kbp	The number of mismatches per 100 kbp	`# mismatches per 100 kbp`	None
\|\|	- -	QUAST	Indels/100kbp	The number of indels per 100 kbp	`# indels per 100 kbp`	None
\|\|	- -	QUAST	Genes	# Genes	`# genes`	gene_count
\|\|	- -	QUAST	Genes (Partial)	# Genes (Partial)	`# genes_partial`	gene_count
\|\|	- -	QUAST	Genome Fraction	The total number of aligned bases in the reference, divided by the genome size.	`Genome fraction (%)`	None

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- Number of Contigs - -

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This plot shows the number of contigs found for each assembly, broken - down by length.

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RSeQC

RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput RNA-seq data.

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- Read GC Content - -

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read_GC calculates a histogram of read GC content.

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BUSCO

BUSCO assesses genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs.

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- Lineage: fungi_odb9 - -

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deepTools

deepTools is a suite of tools to process and analyze deep sequencing data.

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- Filtering metrics - -

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Estimated percentages of alignments filtered independently for each setting in estimateReadFiltering

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Sample Name	M entries	% Aligned	% Tot. Filtered	% Blacklisted	% Missing Flags	% Forbidden Flags	% deepTools Dupes	% Duplication	% Singletons	% Strand Filtered
bismark_se.pbat	30.9	100.0	44.1	0.0	0.0	0.0	43.4	0.0	0.0	5.0
bwameth_se.pbat	71.4	64.7	19.8	0.0	0.0	0.0	28.4	0.0	0.0	6.4

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|	- -	deepTools bamPEFragmentSize	M entries	Number of entries in the file (millions)	`M Entries`	None
\|\|	- -	deepTools bamPEFragmentSize	% Aligned	Percent of aligned entries	`pct_Aligned`	None
\|\|	- -	deepTools bamPEFragmentSize	% Tot. Filtered	Percent of alignment that would be filtered for any reason.	`pct_Filtered`	None
\|\|	- -	deepTools bamPEFragmentSize	% Blacklisted	Percent of alignments falling (at least partially) inside a blacklisted region	`pct_Blacklisted`	None
\|\|	- -	deepTools bamPEFragmentSize	% Missing Flags	Percent of alignments lacking at least on flag specified by --samFlagInclude	`pct_Missing_Flags`	None
\|\|	- -	deepTools bamPEFragmentSize	% Forbidden Flags	Percent of alignments having at least one flag specified by --samFlagExclude	`pct_Forbidden_Flags`	None
\|\|	- -	deepTools bamPEFragmentSize	% deepTools Dupes	Percent of alignments marked by deepTools as being duplicates	`pct_deepTools_Dupes`	None
\|\|	- -	deepTools bamPEFragmentSize	% Duplication	Percent of alignments originally marked as being duplicates	`pct_Duplication`	None
\|\|	- -	deepTools bamPEFragmentSize	% Singletons	Percent of alignments that are singletons (i.e., paired-end reads where the mates don't align as a pair	`pct_Singletons`	None
\|\|	- -	deepTools bamPEFragmentSize	% Strand Filtered	Percent of alignments arising from the wrong strand	`pct_Strand_Filtered`	None

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- Coverage metrics - -

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Sample Name	Min	1st Quartile	Median	Mean	3rd Quartile	Max	Std. Dev.
bismark_se.pbat	0.0	0.0	0.0	3.0	0.0	959.0	16.5
bwameth_se.pbat	0.0	0.0	0.0	4.5	0.0	2589.0	23.4

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|	- -	deepTools plotCoverage	Min	Minimum Coverage	`min`	coverage
\|\|	- -	deepTools plotCoverage	1st Quartile	First quartile coverage	`25%`	coverage
\|\|	- -	deepTools plotCoverage	Median	Median coverage (second quartile)	`50%`	coverage
\|\|	- -	deepTools plotCoverage	Mean	Mean coverage	`mean`	coverage
\|\|	- -	deepTools plotCoverage	3rd Quartile	Third quartile coverage	`75%`	coverage
\|\|	- -	deepTools plotCoverage	Max	Maximum coverage	`max`	coverage
\|\|	- -	deepTools plotCoverage	Std. Dev.	Coverage standard deviation	`std`	coverage

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- Coverage distribution - -

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The fraction of bases with a given number of read/fragment coverage

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- Read lengths - -

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Sample Name	# Sampled	Min	1st Quartile	Mean	Median	3rd Quartile	Max	Std. Dev.
bismark_se.pbat	34118	21	101	99.6	101	101	101	7.1
bwameth_se.pbat	51142	40	101	98.0	101	101	101	10.9
dnmt1MUT_mat2aMUT_1_RGi	15504	148	148	148.0	148	148	148	0.0
dnmt1MUT_mat2aMUT_2_RGi	17327	148	148	148.0	148	148	148	0.0
dnmt1MUT_mat2aMUT_3_RGi	15266	102	148	148.0	148	148	148	0.4

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|	- -	deepTools bamPEFragmentSize	# Sampled	Number of reads sampled	`Reads Sampled`	None
\|\|	- -	deepTools bamPEFragmentSize	Min	Minimum read length	`Read Len. Min.`	read_length
\|\|	- -	deepTools bamPEFragmentSize	1st Quartile	1st quartile read length	`Read Len. 1st. Qu.`	read_length
\|\|	- -	deepTools bamPEFragmentSize	Mean	Mean read length	`Read Len. Mean`	read_length
\|\|	- -	deepTools bamPEFragmentSize	Median	Median read length	`Read Len. Median`	read_length
\|\|	- -	deepTools bamPEFragmentSize	3rd Quartile	3rd quartile read length	`Read Len. 3rd Qu.`	read_length
\|\|	- -	deepTools bamPEFragmentSize	Max	Maximum read length	`Read Len. Max`	read_length
\|\|	- -	deepTools bamPEFragmentSize	Std. Dev.	read length standard deviation	`Read Len. Std.`	read_length
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- Fragment lengths - -

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Sample Name	# Sampled	Min	1st Quartile	Mean	Median	3rd Quartile	Max	Std. Dev.
dnmt1MUT_mat2aMUT_1_RGi	15504	174	185	185	185	185	186	0.2
dnmt1MUT_mat2aMUT_2_RGi	17327	176	185	185	185	185	186	0.2
dnmt1MUT_mat2aMUT_3_RGi	15266	104	185	185	185	185	186	0.7

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|	- -	deepTools bamPEFragmentSize	# Sampled	Number of fragments sampled	`Frag. Sampled`	None
\|\|	- -	deepTools bamPEFragmentSize	Min	Minimum fragment length	`Frag. Len. Min.`	frag_length
\|\|	- -	deepTools bamPEFragmentSize	1st Quartile	1st quartile fragment length	`Frag. Len. 1st. Qu.`	frag_length
\|\|	- -	deepTools bamPEFragmentSize	Mean	Mean fragment length	`Frag. Len. Mean`	frag_length
\|\|	- -	deepTools bamPEFragmentSize	Median	Median fragment length	`Frag. Len. Median`	frag_length
\|\|	- -	deepTools bamPEFragmentSize	3rd Quartile	3rd quartile fragment length	`Frag. Len. 3rd Qu.`	frag_length
\|\|	- -	deepTools bamPEFragmentSize	Max	Maximum fragment length	`Frag. Len. Max`	frag_length
\|\|	- -	deepTools bamPEFragmentSize	Std. Dev.	Fragment length standard deviation	`Frag. Len. Std.`	frag_length
\|\|	- -	deepTools bamPEFragmentSize	MAD	Fragment length median absolute deviation	`Frag. Med. Abs. Dev.`	frag_length

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- Signal enrichment per feature - -

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Signal enrichment per feature according to plotEnrichment

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- Fingerprint - -

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Signal fingerprint according to plotFingerprint

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SnpEff

SnpEff is a genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).

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The stacked bar plot shows locations of detected variants in the genome and the number of variants for each location.

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The upstream and downstream interval size to detect these genomic regions is 5000bp by default.

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The stacked bar plot shows the putative impact of detected variants and the number of variants for each impact.

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There are four levels of impacts predicted by SnpEff:

High: High impact (like stop codon)
Moderate: Middle impact (like same type of amino acid substitution)
Low: Low impact (ie silence mutation)
Modifier: No impact

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The stacked bar plot shows the effect of variants at protein level and the number of variants for each effect type.

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This plot shows the effect of variants on the translation of the mRNA as protein. There are three possible cases:

Silent: The amino acid does not change.
Missense: The amino acid is different.
Nonsense: The variant generates a stop codon.

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Error - was not able to plot data.

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The line plot shows the quantity as function of the variant quality score.

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The quality score corresponds to the QUAL column of the VCF file. This score is set by the variant caller.

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GATK

GATK is a toolkit offering a wide variety of tools with a primary focus on variant discovery and genotyping.

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This plot shows the distribution of base quality scores in each sample before and after base quality score recalibration (BQSR). Applying BQSR should broaden the distribution of base quality scores.

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For more information see the Broad's description of BQSR.

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Sample Name

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HTSeq Count

HTSeq Count is part of the HTSeq Python package - it takes a file with aligned sequencing reads, plus a list of genomic features and counts how many reads map to each feature.

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Bcftools

Bcftools contains utilities for variant calling and manipulating VCFs and BCFs.

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Read depth support distribution for called variants

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featureCounts

Subread featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations.

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Picard

Picard is a set of Java command line tools for manipulating high-throughput sequencing data.

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- Alignment Summary - -

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Plase note that Picard's read counts are divided by two for paired-end data.

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Plot shows the distribution of bases by cycle.

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This plot shows bias in coverage across regions of the genome with varying GC content. A perfect library would be a flat line at y = 1.

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- Insert Size - -

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Plot shows the number of reads at a given insert size. Reads with different orientations are summed.

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Number of bases in primary alignments that align to regions in the reference genome.

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Prokka

Prokka is a software tool for the rapid annotation of prokaryotic genomes.

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This barplot shows the distribution of different types of features found in each contig.

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Prokka can detect different features:

CDS
rRNA
tmRNA
tRNA
miscRNA
signal peptides
CRISPR arrays

This barplot shows you the distribution of these different types of features found in each contig.

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Samblaster

Samblaster is a tool to mark duplicates and extract discordant and split reads from sam files.

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Samtools

Samtools is a suite of programs for interacting with high-throughput sequencing data.

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Alignment metrics from samtools stats; mapped vs. unmapped reads.

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For a set of samples that have come from the same multiplexed library, -similar numbers of reads for each sample are expected. Large differences in numbers might -indicate issues during the library preparation process. Whilst large differences in read -numbers may be controlled for in downstream processings (e.g. read count normalisation), -you may wish to consider whether the read depths achieved have fallen below recommended -levels depending on the applications.

Low alignment rates could indicate contamination of samples (e.g. adapter sequences), -low sequencing quality or other artefacts. These can be further investigated in the -sequence level QC (e.g. from FastQC).

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This module parses the output from samtools stats. All numbers in millions.

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This module parses the output from samtools flagstat. All numbers in millions.

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Bamtools

Bamtools provides both a programmer's API and an end-user's toolkit for handling BAM files.

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VCFTools

VCFTools is a program for working with and reporting on VCF files.

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Plot of TSTV-BY-QUAL - the transition to transversion ratio as a function of SNP quality from the output of vcftools TsTv-by-qual.

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Transition is a purine-to-purine or pyrimidine-to-pyrimidine point mutations. -Transversion is a purine-to-pyrimidine or pyrimidine-to-purine point mutation. -Quality here is the Phred-scaled quality score as given in the QUAL column of VCF. -Note: only bi-allelic SNPs are used (multi-allelic sites and INDELs are skipped.) -Refer to Vcftools's manual (https://vcftools.github.io/man_latest.html) on --TsTv-by-qual

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- - - - - - - - - - - - - - - - diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/post_aligner_soft_stats.tabular --- a/test-data/post_aligner_soft_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,22 +0,0 @@ -Sample QUAST_mqc-generalstats-quast-N50 QUAST_mqc-generalstats-quast-Total_length featureCounts_mqc-generalstats-featurecounts-percent_assigned featureCounts_mqc-generalstats-featurecounts-Assigned Picard_mqc-generalstats-picard-PCT_PF_READS_ALIGNED Prokka_mqc-generalstats-prokka-organism Prokka_mqc-generalstats-prokka-contigs Prokka_mqc-generalstats-prokka-bases Prokka_mqc-generalstats-prokka-CDS Bcftools Stats_mqc-generalstats-bcftools_stats-number_of_records Bcftools Stats_mqc-generalstats-bcftools_stats-number_of_SNPs Bcftools Stats_mqc-generalstats-bcftools_stats-number_of_indels Bcftools Stats_mqc-generalstats-bcftools_stats-tstv Bcftools Stats_mqc-generalstats-bcftools_stats-number_of_MNPs Bamtools_mqc-generalstats-bamtools-duplicates_pct Bamtools_mqc-generalstats-bamtools-mapped_reads_pct Picard_mqc-generalstats-picard-PERCENT_DUPLICATION Picard_mqc-generalstats-picard-summed_median Picard_mqc-generalstats-picard-summed_mean GATK VariantEval_mqc-generalstats-gatk_varianteval-known_titv GATK VariantEval_mqc-generalstats-gatk_varianteval-novel_titv HTSeq Count_mqc-generalstats-htseq_count-percent_assigned HTSeq Count_mqc-generalstats-htseq_count-assigned Picard_mqc-generalstats-picard-PCT_RIBOSOMAL_BASES Picard_mqc-generalstats-picard-PCT_MRNA_BASES Samtools Flagstat_mqc-generalstats-samtools_flagstat-mapped_passed Samtools Stats_mqc-generalstats-samtools_stats-error_rate Samtools Stats_mqc-generalstats-samtools_stats-non_primary_alignments Samtools Stats_mqc-generalstats-samtools_stats-reads_mapped Samtools Stats_mqc-generalstats-samtools_stats-reads_mapped_percent Samtools Stats_mqc-generalstats-samtools_stats-reads_properly_paired_percent Samtools Stats_mqc-generalstats-samtools_stats-reads_MQ0_percent Samtools Stats_mqc-generalstats-samtools_stats-raw_total_sequences SnpEff_mqc-generalstats-snpeff-Change_rate SnpEff_mqc-generalstats-snpeff-Ts_Tv_ratio SnpEff_mqc-generalstats-snpeff-Number_of_variants_before_filter Samblaster_mqc-generalstats-samblaster-pct_dups -14892_1#15 115136.0 18435361.0 -70: TopHat on data 1, data 4, and data 3: accepted_hits 70.82267755353567 321797 -75: TopHat on data 1, data 6, and data 5: accepted_hits 69.58585803304067 445012 -80: TopHat on data 1, data 8, and data 7: accepted_hits 71.76957768385707 394981 -85: TopHat on data 1, data 10, and data 9: accepted_hits 72.02454351337069 437485 -90: TopHat on data 1, data 12, and data 11: accepted_hits 71.33130826437625 388170 -95: TopHat on data 1, data 14, and data 13: accepted_hits 70.72517103678439 453929 -D11_H4K16ac_Rep1_R1_fastq_gz 0.983085 -Sample1 Helicobacter pylori 30 1629978 1548 -Sample2 Escherichia coli 52 162997532523 1548 -Test1 5522770.0 4474244.0 902934.0 1.97 72330.0 -bamtools_txt 0.0 93.125 -dataset_114 0.005582 -dataset_197 176 271.809759 -gatk_varianteval_txt 0.0 2.2 -htseq_txt 0.0 0 -picard_CollectRnaSeqMetrics_bam 79.62310000000001 -samtools_flagstat_txt 20689039 -samtools_stats_txt 0.004248509 12111.0 641821.0 100.0 99.03477760933345 0.010906467691147531 641821.0 -snpeff_csv 3190.0 0.0 972155.0 -virtual-normal 1.28 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/pre_alignment_soft_report.html --- a/test-data/pre_alignment_soft_report.html Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,5990 +0,0 @@ - - - - - - - - - - - - - -MultiQC Report - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

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If you use plots from MultiQC in a publication or presentation, please cite:

- MultiQC: Summarize analysis results for multiple tools and samples in a single report
- Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
- Bioinformatics (2016)
- doi: 10.1093/bioinformatics/btw354
- PMID: 27312411 -

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About MultiQC

This report was generated using MultiQC, version 1.5

You can see a YouTube video describing how to use MultiQC reports here: - https://youtu.be/qPbIlO_KWN0

For more information about MultiQC, including other videos and - extensive documentation, please visit http://multiqc.info

You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: - https://github.com/ewels/MultiQC

MultiQC is published in Bioinformatics:

- MultiQC: Summarize analysis results for multiple tools and samples in a single report
- Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
- Bioinformatics (2016)
- doi: 10.1093/bioinformatics/btw354
- PMID: 27312411 -

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- A modular tool to aggregate results from bioinformatics analyses across many samples into a single report. -

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Report generated on 2018-04-05, 12:06 based on data in: - /Users/bebatut/Documents/galaxy/tools/tools-iuc/tools/multiqc/multiqc_WDir - -

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General Statistics

- - - - - - - - - - Showing ⁶/₆ rows and ⁷/₉ columns. - -

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Sample Name	% Trimmed	% bp Trimmed	% Dropped	% rRNA	% Dups	% GC	Length	% Failed	M Seqs
25839_merged				1.1%
C2			18.0%
dataset_33	10.8%
poulet5_1					36.3%	48%	101 bp	8%	0.3
poulet5_2					36.2%	48%	101 bp	8%	0.3
result_right		45.3%

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Uncheck the tick box to hide columns. Click and drag the handle on the left to change order.

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Sort	Visible	Group	Column	Description	ID	Scale
\|\|	- -	Cutadapt	% Trimmed	% Total Base Pairs trimmed	`percent_trimmed`	None
\|\|	- -	Flexbar	% bp Trimmed	% Total Base Pairs removed	`removed_bases_pct`	None
\|\|	- -	Trimmomatic	% Dropped	% Dropped reads	`dropped_pct`	None
\|\|	- -	SortMeRNA	% rRNA	Percentage of reads matched to a SortMeRNA database	`rRNA_pct`	None
\|\|	- -	FastQC	% Dups	% Duplicate Reads	`percent_duplicates`	None
\|\|	- -	FastQC	% GC	Average % GC Content	`percent_gc`	None
\|\|	- -	FastQC	Length	Average Sequence Length (bp)	`avg_sequence_length`	None
\|\|	- -	FastQC	% Failed	Percentage of modules failed in FastQC report (includes those not plotted here)	`percent_fails`	None
\|\|	- -	FastQC	M Seqs	Total Sequences (millions)	`total_sequences`	read_count

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Cutadapt

Cutadapt is a tool to find and remove adapter sequences, primers, poly-Atails and other types of unwanted sequence from your high-throughput sequencing reads.

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Flexbar

Flexbar is a barcode and adapter removal tool.

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Trimmomatic

Trimmomatic is a flexible read trimming tool for Illumina NGS data.

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SortMeRNA

SortMeRNA is a program for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data.

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FastQC

FastQC is a quality control tool for high throughput sequence data, written by Simon Andrews at the Babraham Institute in Cambridge.

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- Sequence Quality Histograms - -

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The mean quality value across each base position in the read. See the FastQC help.

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- Per Sequence Quality Scores - -

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The number of reads with average quality scores. Shows if a subset of reads has poor quality. See the FastQC help.

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- Per Base Sequence Content - -

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The proportion of each base position for which each of the four normal DNA bases has been called. See the FastQC help.

- - Click a sample row to see a line plot for that dataset. -

Rollover for sample name

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- Position: - -

%T: -

%C: -

%A: -

%G: -

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- Per Sequence GC Content - -

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The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content. - See the FastQC help.

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- Per Base N Content - -

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The percentage of base calls at each position for which an N was called. See the FastQC help.

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- Sequence Length Distribution - -

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All samples have sequences of a single length (101bp).

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- Sequence Duplication Levels - -

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The relative level of duplication found for every sequence. See the FastQC help.

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- Overrepresented sequences - -

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The total amount of overrepresented sequences found in each library. See the FastQC help for further information.

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2 samples had less than 1% of reads made up of overrepresented sequences

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- Adapter Content - -

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The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. See the FastQC help. Only samples with ≥ 0.1% adapter contamination are shown.

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No samples found with any adapter contamination > 0.1%

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- - - - - - - - - - - - - - - - diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/pre_alignment_soft_stats.tabular --- a/test-data/pre_alignment_soft_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,11 +0,0 @@ -Sample SortMeRNA_mqc-generalstats-sortmerna-rRNA_pct Trimmomatic_mqc-generalstats-trimmomatic-dropped_pct fastp_mqc-generalstats-fastp-pct_duplication fastp_mqc-generalstats-fastp-after_filtering_q30_rate fastp_mqc-generalstats-fastp-after_filtering_q30_bases fastp_mqc-generalstats-fastp-after_filtering_gc_content fastp_mqc-generalstats-fastp-pct_surviving fastp_mqc-generalstats-fastp-pct_adapter Cutadapt_mqc-generalstats-cutadapt-percent_trimmed FastQC_mqc-generalstats-fastqc-percent_duplicates FastQC_mqc-generalstats-fastqc-percent_gc FastQC_mqc-generalstats-fastqc-avg_sequence_length FastQC_mqc-generalstats-fastqc-percent_fails FastQC_mqc-generalstats-fastqc-total_sequences Slamdunk_mqc-generalstats-slamdunk-counted Slamdunk_mqc-generalstats-slamdunk-retained Slamdunk_mqc-generalstats-slamdunk-mapped Slamdunk_mqc-generalstats-slamdunk-sequenced Flexbar_mqc-generalstats-flexbar-removed_bases_pct -25839_merged 1.099299750020029 -C2 17.98 -R1_fq 0.0 0.79021 226.0 0.367133 100.0 -bwa-mem-fastq1_fq 0.0 0.907789 41653.0 0.479928 97.97979797979798 33.33333333333333 -dataset_33 10.776820436239396 -poulet5_1 36.30591159931017 48.0 101.0 8.333333333333332 267849.0 -poulet5_2 36.173388748054116 48.0 101.0 8.333333333333332 267849.0 -reads1 16 12 12 12 -reads2 12 6 6 6 -result_right 45.26066350710901 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/prokka_stats.tabular --- a/test-data/prokka_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -Sample repeat_region sig_peptide bases organism tmRNA contigs tRNA rRNA CDS misc_RNA -Sample1 15 88 1629978 Helicobacter pylori 1 30 36 2 1548 -Sample2 162997532523 Escherichia coli 52 2 1548 5152 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/qualimap_bamqc_genome_results.tabular --- a/test-data/qualimap_bamqc_genome_results.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample bam_file total_reads mapped_reads mapped_bases sequenced_bases mean_insert_size median_insert_size mean_mapping_quality general_error_rate percentage_aligned -x_bam x_bam 1248774.0 1242183.0 366875582.0 366823893.0 1097.678 524.0 58.4552 0.0098 99.4722023360512 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/quast_stats.tabular --- a/test-data/quast_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample LG50 # contigs # misassemblies # local misassemblies # misassembled contigs NA50 # genes # indels per 100 kbp Reference length # contigs (>= 10000 bp) Total length (>= 1000 bp) GC (%) Reference GC (%) Unaligned length Misassembled contigs length Genome fraction (%) Largest alignment L75 NG75 # contigs (>= 1000 bp) Largest contig N75 NGA50 NA75 LA50 LGA75 Total length LG75 Total length (>= 50000 bp) # contigs (>= 50000 bp) # mismatches per 100 kbp Total length (>= 25000 bp) Total length (>= 10000 bp) Total length (>= 5000 bp) Total length (>= 0 bp) # unaligned contigs_partial # contigs (>= 25000 bp) LA75 # contigs (>= 0 bp) N50 LGA50 # genes_partial NGA75 # contigs (>= 5000 bp) Duplication ratio NG50 # unaligned contigs # N's per 100 kbp L50 -14892_1#15 50.0 467.0 107.0 132.0 82.0 102129.0 7280.0 33.75 18916112.0 215.0 18373173.0 48.17 48.21 88446.0 4540800.0 95.482 356982.0 100.0 56990.0 376.0 435484.0 62262.0 99244.0 54365.0 56.0 124.0 18435361.0 106.0 15112131.0 123.0 262.21 17353907.0 17893099.0 18079934.0 18465341.0 59.0 181.0 117.0 545.0 115136.0 59.0 968.0 51757.0 242.0 1.016 112874.0 8.0 929.55 48.0 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/rsem.txt --- a/test-data/rsem.txt Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,57 +0,0 @@ -2302013 30752387 0 33054400 -30113921 638466 13832652 -65457099 3 -0 2302013 -1 16919735 -2 6224666 -3 3186612 -4 1664884 -5 1091224 -6 555346 -7 358669 -8 245597 -9 98797 -10 65875 -11 83793 -12 46956 -13 26998 -14 45559 -15 33388 -16 11464 -17 7678 -18 12949 -19 22852 -20 16386 -21 6725 -22 16252 -23 3943 -24 3304 -25 18 -26 1 -27 11 -28 27 -29 37 -30 56 -31 115 -32 146 -33 210 -34 18 -35 128 -36 5 -37 47 -38 129 -39 81 -40 1231 -41 284 -42 27 -43 112 -44 6 -45 4 -46 1 -47 1 -48 7 -53 2 -71 24 -73 1 -77 6 -Inf 0 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/salmon_flenDist.txt --- a/test-data/salmon_flenDist.txt Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -8.54794e-14 8.88776e-14 9.23963e-14 9.60394e-14 9.98106e-14 1.03714e-13 1.07752e-13 1.11931e-13 1.16253e-13 1.20724e-13 1.25347e-13 1.30126e-13 1.35067e-13 1.40173e-13 1.4545e-13 1.50902e-13 1.56533e-13 1.6235e-13 1.68356e-13 1.74557e-13 1.80958e-13 1.87565e-13 1.94382e-13 2.01416e-13 2.08672e-13 2.16156e-13 2.23872e-13 2.31828e-13 2.4003e-13 2.48482e-13 2.57192e-13 2.66166e-13 2.7541e-13 2.8493e-13 2.94734e-13 3.04827e-13 3.15216e-13 3.25909e-13 3.36912e-13 3.48231e-13 3.59875e-13 3.7185e-13 3.84164e-13 3.96823e-13 4.09835e-13 4.23208e-13 4.36949e-13 4.51066e-13 4.65566e-13 4.80457e-13 4.95747e-13 5.11443e-13 5.27555e-13 5.44088e-13 5.61052e-13 5.78455e-13 5.96304e-13 6.14608e-13 6.33375e-13 6.52613e-13 6.7233e-13 6.92535e-13 7.13235e-13 7.34439e-13 7.56156e-13 7.78393e-13 8.01159e-13 8.24462e-13 8.4831e-13 8.72712e-13 8.97675e-13 9.23208e-13 9.49319e-13 9.76016e-13 1.00331e-12 1.0312e-12 1.0597e-12 1.08882e-12 1.11857e-12 1.14895e-12 1.17997e-12 1.21163e-12 1.24396e-12 1.27694e-12 1.3106e-12 1.34493e-12 1.37995e-12 1.41566e-12 1.45206e-12 1.48917e-12 1.52699e-12 1.56552e-12 1.60477e-12 1.64476e-12 1.68547e-12 1.72692e-12 1.76912e-12 1.81206e-12 3.29651e-05 0.00018966 0.000505733 0.000852837 0.00107903 0.00117955 0.0012102 0.00118557 0.00113454 0.00110862 0.00112071 0.001135 0.00112018 0.00109392 0.00110592 0.00116328 0.00120188 0.00119639 0.00120395 0.00123364 0.00121303 0.00113283 0.00106575 0.0010294 0.00101907 0.00107787 0.00117117 0.00122155 0.00126292 0.001322 0.00132568 0.00125944 0.0012187 0.00122729 0.00122764 0.00125145 0.00130243 0.00129889 0.00129122 0.00136001 0.00143294 0.00144178 0.00141998 0.00139328 0.00136291 0.00137291 0.00143527 0.00148261 0.00148996 0.0014951 0.00152389 0.00155437 0.00155677 0.00157319 0.00161304 0.00161234 0.00155184 0.00146051 0.00140614 0.00145661 0.00161047 0.00177332 0.00183641 0.00180834 0.00175883 0.00171746 0.00167723 0.00163458 0.00160951 0.00161254 0.00166641 0.00181422 0.00201421 0.00213023 0.00209065 0.00197041 0.00188134 0.00184267 0.00181737 0.00181102 0.00185763 0.00195455 0.00203258 0.00205324 0.00208063 0.00211824 0.00209545 0.00206314 0.00209033 0.00209553 0.00204238 0.00203362 0.00209684 0.00217598 0.00227147 0.00238701 0.00243673 0.00232052 0.00213204 0.00209969 0.00224284 0.00240577 0.00252668 0.0025933 0.002587 0.00256927 0.00259717 0.00263285 0.00263222 0.00258247 0.00252205 0.00252088 0.00256024 0.00259275 0.0026236 0.00266515 0.00270772 0.0027058 0.00268944 0.0027414 0.00278318 0.00271033 0.00262591 0.0026647 0.00279403 0.00290929 0.00296039 0.00295669 0.00293271 0.0028987 0.0028311 0.00277538 0.00282072 0.00293968 0.00304533 0.00310031 0.00310671 0.00309913 0.00308228 0.00302181 0.00292959 0.00285281 0.00281429 0.00282158 0.00288 0.00296587 0.00307507 0.00321613 0.00327918 0.00318075 0.00306869 0.00304228 0.00299811 0.00295958 0.0030338 0.00314258 0.0032122 0.00330145 0.00337388 0.00331331 0.00319232 0.00317648 0.00324005 0.00325072 0.0032239 0.0032372 0.00321137 0.00309323 0.00303576 0.00311229 0.00316625 0.00309878 0.00297703 0.00288252 0.00287056 0.00294284 0.00301172 0.00296646 0.00283922 0.00281166 0.00291487 0.00303261 0.00313036 0.00314853 0.00305521 0.00298739 0.00299062 0.00297359 0.00291442 0.00284123 0.00280557 0.00284507 0.00290229 0.00289053 0.00282273 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9.40549e-07 1.21916e-06 7.48889e-07 1.77639e-07 8.48451e-20 8.48451e-20 3.74019e-10 1.24594e-07 4.9984e-07 1.65769e-06 4.85254e-06 8.49019e-06 8.04065e-06 3.86231e-06 7.51093e-07 3.88541e-08 1.42289e-07 3.74887e-07 5.13763e-07 5.22964e-07 1.3609e-06 3.23852e-06 3.92375e-06 2.4373e-06 1.49085e-06 2.52107e-06 3.62893e-06 3.89446e-06 3.4838e-06 2.38137e-06 2.43245e-06 4.29959e-06 5.14334e-06 4.42458e-06 5.07748e-06 7.05396e-06 6.70794e-06 3.56321e-06 1.09354e-06 5.94004e-07 2.23031e-06 6.82104e-06 9.6855e-06 6.31699e-06 1.55824e-06 2.43299e-08 9.73194e-08 1.45979e-07 9.73194e-08 2.43299e-08 5.65959e-07 2.86045e-06 5.78219e-06 5.87574e-06 3.0814e-06 7.90119e-07 4.3638e-07 1.26769e-06 1.86803e-06 3.32101e-06 8.55452e-06 1.2341e-05 8.22336e-06 2.0626e-06 2.28594e-07 8.46747e-07 1.23631e-06 8.12933e-07 2.01542e-07 8.48451e-20 6.62153e-07 2.64861e-06 3.97306e-06 2.64918e-06 6.63001e-07 5.65634e-10 1.41408e-10 5.08647e-07 2.69674e-06 5.74233e-06 6.20182e-06 3.51613e-06 9.91274e-07 1.49684e-07 2.94087e-08 9.78813e-09 1.46822e-08 2.48321e-08 1.24873e-07 4.67214e-07 9.51419e-07 1.05552e-06 6.09723e-07 1.51734e-07 8.0021e-09 8.22241e-09 7.6778e-07 3.48633e-06 6.56158e-06 6.56591e-06 3.83529e-06 1.87558e-06 2.86313e-06 5.46522e-06 6.77583e-06 6.76114e-06 5.96453e-06 3.46521e-06 8.60546e-07 8.57557e-07 3.41456e-06 5.12027e-06 3.97947e-06 3.37465e-06 5.5051e-06 8.12692e-06 8.17751e-06 4.99229e-06 1.70417e-06 4.16364e-07 1.04091e-07 8.48451e-20 8.48451e-20 1.03855e-06 4.17877e-06 7.31893e-06 8.25894e-06 7.07274e-06 3.98182e-06 1.10885e-06 4.78174e-07 7.17261e-07 4.78174e-07 1.06162e-06 3.76832e-06 5.65248e-06 3.76832e-06 1.00433e-06 9.46158e-07 3.69878e-06 6.57856e-06 6.0715e-06 2.84656e-06 5.40835e-07 6.62769e-07 2.64063e-06 3.95989e-06 2.63993e-06 6.65929e-07 2.3786e-08 3.5679e-08 2.3786e-08 5.9465e-09 8.48451e-20 8.48451e-20 1.05325e-06 4.213e-06 6.31951e-06 4.213e-06 1.74237e-06 2.75646e-06 4.14557e-06 2.79999e-06 7.54417e-07 4.35348e-08 1.08837e-08 1.62467e-06 6.4987e-06 9.74804e-06 6.4987e-06 1.62467e-06 2.42376e-07 9.69503e-07 1.45515e-06 9.73101e-07 2.47772e-07 3.59728e-09 2.08228e-06 8.32552e-06 1.25152e-05 8.43337e-06 2.53305e-06 1.26743e-06 1.76634e-06 1.16823e-06 9.73446e-07 2.64779e-06 3.92848e-06 2.60459e-06 6.81238e-07 1.34953e-07 2.17296e-07 1.64686e-07 5.60377e-08 2.95843e-07 1.15959e-06 1.82339e-06 2.39241e-06 4.38112e-06 6.7061e-06 7.6585e-06 6.95299e-06 4.13776e-06 1.10966e-06 5.44951e-07 2.05945e-06 3.08987e-06 2.06224e-06 5.19564e-07 4.87571e-09 1.20166e-07 4.67429e-07 7.15222e-07 5.67288e-07 3.57226e-07 7.34211e-07 1.98274e-06 2.77314e-06 1.8253e-06 5.34391e-07 3.12261e-07 4.68391e-07 3.12261e-07 7.80652e-08 4.91325e-08 1.9653e-07 2.94795e-07 1.96778e-07 5.01263e-08 1.49069e-09 9.9379e-10 2.48448e-10 8.48451e-20 8.48451e-20 1.28319e-06 5.13871e-06 7.72294e-06 5.16845e-06 1.30698e-06 5.9465e-09 6.45033e-08 4.1415e-07 1.01157e-06 1.21721e-06 7.78569e-07 2.90415e-07 8.9519e-08 1.62661e-06 7.55928e-06 1.41948e-05 1.33201e-05 6.37014e-06 1.43714e-06 1.9653e-07 4.91325e-08 8.48451e-20 1.40225e-09 3.01961e-08 1.06762e-07 1.53132e-07 1.48883e-07 2.21117e-07 2.94795e-07 1.9653e-07 1.52023e-07 1.4224e-06 4.66068e-06 6.47657e-06 4.14623e-06 1.2079e-06 7.88265e-07 1.1824e-06 7.88265e-07 1.97066e-07 1.13356e-09 4.53426e-09 7.40038e-08 8.39303e-07 2.66819e-06 3.66457e-06 2.33104e-06 5.65959e-07 8.48451e-20 5.75979e-08 2.30392e-07 3.45587e-07 2.32447e-07 6.58203e-08 1.23336e-08 1.27549e-08 2.01854e-08 2.71947e-08 1.81298e-08 4.53244e-09 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 1.56137e-07 6.82145e-07 1.16721e-06 9.70134e-07 3.86528e-07 5.75979e-08 9.89308e-07 3.95723e-06 5.95252e-06 4.56652e-06 3.25974e-06 3.32229e-06 2.6434e-06 2.3679e-06 2.73795e-06 1.8253e-06 4.56325e-07 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 4.52923e-08 1.81169e-07 2.71754e-07 1.81169e-07 4.52923e-08 8.48451e-20 2.42376e-07 9.69503e-07 1.45426e-06 9.69503e-07 2.42376e-07 8.48451e-20 1.27948e-07 5.11793e-07 7.72222e-07 5.29923e-07 3.56237e-07 8.22506e-07 1.2111e-06 8.04377e-07 2.01094e-07 1.19543e-07 4.85833e-07 7.47897e-07 5.59316e-07 2.9093e-07 2.18785e-07 1.4075e-07 3.51876e-08 8.48451e-20 1.7085e-09 6.83399e-09 1.0251e-08 4.48392e-07 1.76794e-06 2.64935e-06 1.76623e-06 4.41558e-07 2.28063e-07 9.20891e-07 1.40294e-06 9.70858e-07 3.1919e-07 1.67271e-07 2.04131e-07 9.36586e-07 3.27659e-06 4.87062e-06 3.25897e-06 8.59342e-07 7.1358e-08 4.7572e-08 1.1893e-08 8.48451e-20 1.19543e-07 4.78174e-07 7.17261e-07 4.78174e-07 1.19543e-07 8.48451e-20 8.48451e-20 8.48451e-20 3.652e-07 1.4608e-06 2.1912e-06 1.4608e-06 3.652e-07 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 2.88646e-09 1.31089e-07 4.95492e-07 7.28806e-07 4.8106e-07 1.19543e-07 8.48451e-20 2.11966e-06 8.47864e-06 1.2718e-05 8.49079e-06 2.16829e-06 3.62843e-07 1.88217e-06 4.44733e-06 5.20328e-06 2.98569e-06 6.76004e-07 8.22241e-09 1.23336e-08 8.22241e-09 4.1112e-09 8.22241e-09 1.23336e-08 8.22241e-09 2.0556e-09 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 5.08647e-07 2.89843e-06 6.66338e-06 7.84217e-06 4.90082e-06 2.61356e-05 9.87451e-05 0.000147884 - diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/salmon_meta_info.json --- a/test-data/salmon_meta_info.json Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,15 +0,0 @@ -{ - "salmon_version": "0.6.0", - "samp_type": "none", - "frag_dist_length": 2001, - "bias_correct": true, - "num_bias_bins": 4096, - "mapping_type": "mapping", - "num_targets": 209539, - "num_bootstraps": 0, - "num_processed": 439147, - "num_mapped": 367866, - "percent_mapped": 83.76830537382699, - "call": "quant", - "start_time": "Thu Mar 31 13:09:43 2016" -} \ No newline at end of file diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/samblaster_stats.tabular --- a/test-data/samblaster_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample n_nondups n_tot n_dups pct_dups -virtual-normal 77 78 1 1.28 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/samtools_flagstat_stats.tabular --- a/test-data/samtools_flagstat_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample read2_passed mapped_failed_pct with mate mapped to a different chr (mapQ >= 5)_passed properly paired_passed read1_passed total_passed supplementary_failed duplicates_failed singletons_failed mapped_passed_pct secondary_passed properly paired_passed_pct properly paired_failed_pct singletons_passed with mate mapped to a different chr (mapQ >= 5)_failed supplementary_passed duplicates_passed flagstat_total mapped_passed with mate mapped to a different chr_failed secondary_failed properly paired_failed with itself and mate mapped_failed with mate mapped to a different chr_passed paired in sequencing_failed with itself and mate mapped_passed singletons_passed_pct total_failed paired in sequencing_passed read1_failed mapped_failed read2_failed singletons_failed_pct -samtools_flagstat 0 nan 0 0 0 21040602 0 0 0 98.33 0 nan nan 0 0 0 5448463 21040602 20689039 0 0 0 0 0 0 0 nan 0 0 0 0 0 nan diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/samtools_stats_stats.tabular --- a/test-data/samtools_stats_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample is_sorted insert_size_standard_deviation reads_paired_percent reads_QC_failed bases_mapped 1st_fragments reads_mapped_and_paired_percent error_rate mismatches reads_properly_paired bases_mapped_(cigar) reads_MQ0 reads_duplicated reads_duplicated_percent inward_oriented_pairs sequences non-primary_alignments reads_MQ0_percent reads_mapped_percent reads_mapped_and_paired average_length last_fragments average_quality outward_oriented_pairs total_length bases_duplicated raw_total_sequences bases_trimmed pairs_on_different_chromosomes reads_properly_paired_percent reads_mapped reads_unmapped_percent maximum_length reads_paired reads_QC_failed_percent insert_size_average reads_unmapped filtered_sequences pairs_with_other_orientation -samtools_stats 1.0 1223.0 100.0 0.0 64823921.0 320981.0 99.52089445499603 0.004248509 275405.0 635626.0 64823921.0 70.0 0.0 0.0 317512.0 641821.0 12111.0 0.010906467691147531 100.0 638746.0 101.0 320840.0 26.0 1294.0 64823921.0 0.0 641821.0 0.0 0.0 99.03477760933345 641821.0 0.0 101.0 641821.0 0.0 719.7 0.0 0.0 30.0 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/slamdunk_readrates_plus.tabular --- a/test-data/slamdunk_readrates_plus.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ -Sample A>C A>G A>T C>A C>G C>T G>A G>C G>T T>A T>C T>G -slamdunk_reads1_overallrates_csv 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.7735849056603774 0.0 -slamdunk_reads2_overallrates_csv 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 3.260869565217391 0.0 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/snpeff_stats.tabular --- a/test-data/snpeff_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample MODERATE splice_donor_variant+splice_region_variant+5_prime_UTR_variant+intron_variant_percent splice_region_variant+non_coding_exon_variant frameshift_variant+splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant_percent frameshift_variant+splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant splice_donor_variant+splice_region_variant+5_prime_UTR_variant+intron_variant frameshift_variant+start_lost+splice_region_variant_percent NONE intragenic_variant_percent splice_region_variant+non_coding_exon_variant_percent UTR_3_PRIME splice_donor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent splice_acceptor_variant+splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant Ts_Tv_ratio splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent inframe_insertion+splice_region_variant_percent UTR_3_PRIME_percent inframe_deletion+splice_region_variant 5_prime_UTR_truncation+exon_loss_variant disruptive_inframe_deletion_percent INTRON LOW Het start_lost+disruptive_inframe_insertion frameshift_variant+splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant_percent inframe_deletion splice_acceptor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent non_coding_exon_variant frameshift_variant+stop_gained splice_acceptor_variant+splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent DOWNSTREAM_percent disruptive_inframe_deletion+splice_region_variant MOTIF frameshift_variant+start_lost+splice_region_variant splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant frameshift_variant+stop_gained_percent EXON splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant upstream_gene_variant intron_variant_percent splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent inframe_deletion_percent HIGH_percent 3_prime_UTR_variant splice_donor_variant+intron_variant frameshift_variant+start_lost_percent disruptive_inframe_insertion non_coding_exon_variant_percent Change_rate 5_prime_UTR_truncation+exon_loss_variant_percent MODERATE_percent splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent UTR_5_PRIME TRANSCRIPT frameshift_variant downstream_gene_variant MODIFIER_percent splice_acceptor_variant+inframe_deletion+splice_region_variant+splice_region_variant+intron_variant_percent LOW_percent frameshift_variant+splice_region_variant Missense_Silent_ratio Missing disruptive_inframe_deletion+splice_region_variant_percent splice_acceptor_variant+disruptive_inframe_deletion+splice_region_variant+splice_region_variant+intron_variant_percent frameshift_variant+stop_lost frameshift_variant+splice_acceptor_variant+splice_region_variant+intron_variant sequence_feature_percent intron_variant frameshift_variant+splice_region_variant_percent splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant splice_donor_variant+5_prime_UTR_variant+intron_variant Number_of_known_variants
(i.e. non-empty ID)_percent start_lost+disruptive_inframe_insertion_percent splice_acceptor_variant+splice_donor_variant+intron_variant Transitions DOWNSTREAM SPLICE_SITE_DONOR_percent frameshift_variant+stop_lost_percent splice_acceptor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant_percent splice_acceptor_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent EXON_percent frameshift_variant_percent Number_of_variants_before_filter disruptive_inframe_insertion_percent splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant_percent splice_acceptor_variant+intron_variant stop_gained+inframe_insertion upstream_gene_variant_percent SPLICE_SITE_ACCEPTOR TF_binding_site_variant_percent SPLICE_SITE_REGION Genome_effective_length frameshift_variant+splice_acceptor_variant+splice_region_variant+intron_variant_percent splice_acceptor_variant+5_prime_UTR_variant+intron_variant INTERGENIC_percent splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant 5_prime_UTR_variant UPSTREAM_percent splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant splice_acceptor_variant+disruptive_inframe_deletion+splice_region_variant+splice_region_variant+intron_variant splice_acceptor_variant+splice_region_variant+intron_variant 5_prime_UTR_variant_percent Type splice_acceptor_variant+inframe_deletion+splice_region_variant+splice_region_variant+intron_variant Hom splice_donor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant splice_region_variant+splice_region_variant_percent UTR_5_PRIME_percent sequence_feature intergenic_region_percent transcript_percent HIGH frameshift_variant+splice_donor_variant+splice_region_variant+intron_variant UPSTREAM splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent inframe_deletion+splice_region_variant_percent transcript splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent Genome_total_length Number_of_effects NONE_percent frameshift_variant+splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant SPLICE_SITE_ACCEPTOR_percent splice_acceptor_variant+intron_variant_percent splice_donor_variant+intron_variant_percent splice_donor_variant+5_prime_UTR_variant+intron_variant_percent splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant_percent splice_acceptor_variant+splice_donor_variant+intron_variant_percent splice_donor_variant+splice_region_variant+intron_variant splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant_percent Transversions Genome disruptive_inframe_deletion MODIFIER splice_acceptor_variant+splice_region_variant+intron_variant_percent frameshift_variant+start_lost SPLICE_SITE_REGION_percent splice_acceptor_variant+splice_region_variant+intron_variant+non_coding_exon_variant INTRON_percent splice_acceptor_variant+5_prime_UTR_variant+intron_variant_percent splice_acceptor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant TF_binding_site_variant MOTIF_percent frameshift_variant+splice_donor_variant+splice_region_variant+intron_variant_percent inframe_insertion splice_region_variant+intron_variant stop_gained+inframe_insertion_percent inframe_insertion+splice_region_variant Number_of_known_variants
(i.e. non-empty ID) splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant 3_prime_UTR_variant_percent splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant_percent downstream_gene_variant_percent INTERGENIC splice_acceptor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant splice_region_variant+splice_region_variant splice_donor_variant+splice_region_variant+intron_variant_percent splice_region_variant splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant splice_region_variant+intron_variant_percent splice_region_variant_percent SPLICE_SITE_DONOR inframe_insertion_percent intergenic_region TRANSCRIPT_percent intragenic_variant -snpeff 3322.0 1.8e-05 462.0 0.000109 1.0 1.0 1.8e-05 2174772.0 0.004855 0.0084 15811.0 1.8e-05 2.0 0.0 9.1e-05 3.6e-05 0.287478 10.0 2.0 0.007418 2126738.0 2178258.0 524875.0 1.0 1.8e-05 159.0 0.000127 15320.0 21.0 3.6e-05 6.178119 2.0 986.0 1.0 3.0 0.000382 17369.0 1.0 354347.0 38.668709 1.8e-05 0.002891 0.024855 15811.0 41.0 0.000145 277.0 0.278551 3190.0 3.6e-05 0.060401 1.8e-05 3352.0 1.0 800.0 339790.0 60.30929 1.8e-05 39.605454 77.0 ? 0.0 3.6e-05 1.8e-05 3.0 2.0 39.535817 2126738.0 0.0014 13.0 2.0 78.616167 1.8e-05 61.0 0.0 339790.0 0.001473 5.5e-05 3.6e-05 9.1e-05 0.315806 0.014546 972155.0 0.005036 5.5e-05 224.0 3.0 6.442797 360.0 0.017928 5040.0 3101536026.0 3.6e-05 2.0 8.386471 5.0 3350.0 6.442797 12.0 1.0 32.0 0.06091 Count 1.0 392480.0 1.0 1.8e-05 0.060947 2174428.0 8.386471 0.0014 1367.0 3.0 354347.0 0.000236 0.000182 77.0 9.1e-05 32036512383.0 5499894.0 39.542071 6.0 0.006546 0.004073 0.000745 3.6e-05 0.000218 0.001109 15.0 1.8e-05 0.0 GRCh37.75 408.0 3316947.0 0.000582 8.0 0.091638 5.0 38.668709 3.6e-05 7.0 986.0 0.017928 5.5e-05 266.0 4390.0 5.5e-05 2.0 764271.0 5.0 0.287478 1.0 5.5e-05 6.178119 461247.0 2.0 1.0 0.000273 187.0 3.0 1.0 0.07982 0.0034 81.0 0.004836 461247.0 1.8e-05 267.0 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/sortmerna_stats.tabular --- a/test-data/sortmerna_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample silva-euk-28s-id98_count silva-arc-16s-id95_count silva-euk-18s-id95_pct silva-bac-23s-id98_pct silva-arc-23s-id98_pct rfam-5s-database-id98_count rRNA_pct silva-bac-16s-id90_count rfam-5.8s-database-id98_count silva-euk-18s-id95_count rRNA silva-euk-28s-id98_pct silva-arc-16s-id95_pct total rfam-5s-database-id98_pct non_rRNA_pct rfam-5.8s-database-id98_pct silva-bac-23s-id98_count silva-arc-23s-id98_count silva-bac-16s-id90_pct non_rRNA -25839_merged 444.35560000000004 0.0 0.25 0.24 0.0 0.0 1.099299750020029 26216.9804 0.0 11108.89 48848 0.01 0.0 4443556 0.0 98.90070024997996 0.0 10664.534399999999 0.0 0.59 4394708 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/star_stats.tabular --- a/test-data/star_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample mismatch_rate avg_input_read_length num_annotated_splices multimapped_toomany_percent num_splices uniquely_mapped uniquely_mapped_percent multimapped multimapped_toomany unmapped_tooshort multimapped_percent num_ATAC_splices unmapped_tooshort_percent total_reads unmapped_mismatches num_noncanonical_splices insertion_rate unmapped_other_percent num_GTAG_splices insertion_length deletion_length deletion_rate unmapped_other unmapped_mismatches_percent num_GCAG_splices avg_mapped_read_length -star_log 1.73 75.0 0.0 0.0 47.0 89.0 89.0 1.0 0.0 10 1.0 0.0 10.0 100.0 0 0.0 0.0 0.0 47.0 0.0 0.0 0.0 0 0.0 0.0 74.8 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/tophat_stats.tabular --- a/test-data/tophat_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample total_reads concordant_aligned_percent unaligned_total aligned_total aligned_multimap aligned_discordant overall_aligned_percent aligned_not_multimapped_discordant -tophat_align 316390.0 99.0 2985.0 313405.0 5638.0 34.0 99.5 307733.0 diff -r f7985e0479b9 -r c1a4b5f3b432 test-data/trimmomatic_stats.tabular --- a/test-data/trimmomatic_stats.tabular Sat Nov 21 12:54:24 2020 +0000 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -Sample input_reads surviving dropped surviving_pct dropped_pct -C2 39733090.0 32590558.0 7142532.0 82.02 17.98

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