# HG changeset patch
# User iuc
# Date 1538177429 14400
# Node ID db1eeffba23e9bfe3b088f1df2ee415a62d2bb19
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nanoplot/ commit ad3c2e459ae53ab61df3d967d755fd0b42149328
diff -r 000000000000 -r db1eeffba23e nanoplot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/nanoplot.xml Fri Sep 28 19:30:29 2018 -0400
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+ Plotting suite for Oxford Nanopore sequencing data and alignments
+
+ nanoplot
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+ @misc{githubnanoplot, author = {De Coster, Wouter}, year = {2018}, title =
+ {NanoPlot}, publisher = {GitHub}, journal = {GitHub repository}, url =
+ {https://github.com/wdecoster/NanoPlot}, }
+ 10.1093/bioinformatics/bty149
+
+
diff -r 000000000000 -r db1eeffba23e test-data/HistogramReadlength.jpg
Binary file test-data/HistogramReadlength.jpg has changed
diff -r 000000000000 -r db1eeffba23e test-data/NanoPlot-report.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NanoPlot-report.html Fri Sep 28 19:30:29 2018 -0400
@@ -0,0 +1,362 @@
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+
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+ NanoPlot Report
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+ NanoPlot report
+
Summary statistics prior to filtering
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+|
+
+ | General summary: |
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+ | Active channels: | 169 |
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+
+ | Mean read length: | 23212.6 |
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+ | Mean read quality: | 10.1 |
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+ | Median read length: | 9390.0 |
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+ | Median read quality: | 10.3 |
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+ | Number of reads: | 371 |
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+ | Read length N50: | 60395 |
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+ | Total bases: | 8611871 |
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+|
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+ | Number, percentage and megabases of reads above quality cutoffs |
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+ | >Q5: | 371 (100.0%) 8.6Mb |
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+ | >Q7: | 371 (100.0%) 8.6Mb |
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+ | >Q10: | 207 (55.8%) 4.7Mb |
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+ | >Q12: | 49 (13.2%) 0.9Mb |
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+ | >Q15: | 0 (0.0%) 0.0Mb |
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+|
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+ | Top 5 highest mean basecall quality scores and their read lengths |
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+ | 1: | 13.3 (6333) |
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+ | 2: | 13.1 (5448) |
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+ | 3: | 12.9 (27834) |
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+ | 4: | 12.8 (20351) |
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+ | 5: | 12.8 (97730) |
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+|
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+ | Top 5 longest reads and their mean basecall quality score |
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+ | 1: | 393431 (10.6) |
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+ | 2: | 341725 (11.8) |
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+ | 3: | 320662 (8.0) |
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+ | 4: | 226843 (9.1) |
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+ | 5: | 221901 (10.0) |
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+
Summary statistics after filtering
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+|
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+ | General summary: |
+
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+ | Active channels: | 169 |
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+ | Mean read length: | 23212.6 |
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+ | Mean read quality: | 10.1 |
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+ | Median read length: | 9390.0 |
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+ | Median read quality: | 10.3 |
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+ | Number of reads: | 371 |
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+ | Read length N50: | 60395 |
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+ | Total bases: | 8611871 |
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+|
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+ | Number, percentage and megabases of reads above quality cutoffs |
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+ | >Q5: | 371 (100.0%) 8.6Mb |
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+ | >Q7: | 371 (100.0%) 8.6Mb |
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+ | >Q10: | 207 (55.8%) 4.7Mb |
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+ | >Q12: | 49 (13.2%) 0.9Mb |
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+ | >Q15: | 0 (0.0%) 0.0Mb |
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+
+|
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+ | Top 5 highest mean basecall quality scores and their read lengths |
+
+
+ | 1: | 13.3 (6333) |
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+ | 2: | 13.1 (5448) |
+
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+ | 3: | 12.9 (27834) |
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+ | 4: | 12.8 (20351) |
+
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+ | 5: | 12.8 (97730) |
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+
+|
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+ | Top 5 longest reads and their mean basecall quality score |
+
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+ | 1: | 393431 (10.6) |
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+ | 2: | 341725 (11.8) |
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+ | 3: | 320662 (8.0) |
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+ | 4: | 226843 (9.1) |
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+ | 5: | 221901 (10.0) |
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Plots
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Histogram of read lengths
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Weighted Histogram of read lengths
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Yield by length
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Read lengths vs Average read quality plot using hexagonal bins
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Read lengths vs Average read quality plot using a kernel density estimation
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Number of reads generated per channel
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Cumulative yield
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Cumulative yield
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Number of reads over time
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Number of active pores over time
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Violin plot of read lengths over time
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Violin plot of quality over time
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\ No newline at end of file
diff -r 000000000000 -r db1eeffba23e test-data/NanoStats.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NanoStats.txt Fri Sep 28 19:30:29 2018 -0400
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+General summary:
+Active channels: 169
+Mean read length: 23212.6
+Mean read quality: 10.1
+Median read length: 9390.0
+Median read quality: 10.3
+Number of reads: 371
+Read length N50: 60395
+Total bases: 8611871
+Number, percentage and megabases of reads above quality cutoffs
+>Q5: 371 (100.0%) 8.6Mb
+>Q7: 371 (100.0%) 8.6Mb
+>Q10: 207 (55.8%) 4.7Mb
+>Q12: 49 (13.2%) 0.9Mb
+>Q15: 0 (0.0%) 0.0Mb
+Top 5 highest mean basecall quality scores and their read lengths
+1: 13.3 (6333)
+2: 13.1 (5448)
+3: 12.9 (27834)
+4: 12.8 (20351)
+5: 12.8 (97730)
+Top 5 longest reads and their mean basecall quality score
+1: 393431 (10.6)
+2: 341725 (11.8)
+3: 320662 (8.0)
+4: 226843 (9.1)
+5: 221901 (10.0)
diff -r 000000000000 -r db1eeffba23e test-data/NanoStats_post_filtering.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/NanoStats_post_filtering.txt Fri Sep 28 19:30:29 2018 -0400
@@ -0,0 +1,27 @@
+General summary:
+Active channels: 169
+Mean read length: 23212.6
+Mean read quality: 10.1
+Median read length: 9390.0
+Median read quality: 10.3
+Number of reads: 371
+Read length N50: 60395
+Total bases: 8611871
+Number, percentage and megabases of reads above quality cutoffs
+>Q5: 371 (100.0%) 8.6Mb
+>Q7: 371 (100.0%) 8.6Mb
+>Q10: 207 (55.8%) 4.7Mb
+>Q12: 49 (13.2%) 0.9Mb
+>Q15: 0 (0.0%) 0.0Mb
+Top 5 highest mean basecall quality scores and their read lengths
+1: 13.3 (6333)
+2: 13.1 (5448)
+3: 12.9 (27834)
+4: 12.8 (20351)
+5: 12.8 (97730)
+Top 5 longest reads and their mean basecall quality score
+1: 393431 (10.6)
+2: 341725 (11.8)
+3: 320662 (8.0)
+4: 226843 (9.1)
+5: 221901 (10.0)
diff -r 000000000000 -r db1eeffba23e test-data/alignment.bam
Binary file test-data/alignment.bam has changed
diff -r 000000000000 -r db1eeffba23e test-data/bam-LogTransformed_HistogramReadlength.svg
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam-LogTransformed_HistogramReadlength.svg Fri Sep 28 19:30:29 2018 -0400
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diff -r 000000000000 -r db1eeffba23e test-data/bam-report.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bam-report.html Fri Sep 28 19:30:29 2018 -0400
@@ -0,0 +1,401 @@
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+
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+ NanoPlot Report
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+ NanoPlot report
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Summary statistics prior to filtering
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+ | General summary: |
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+ | Average percent identity: | 85.3 |
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+ | Mean read length: | 12291.0 |
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+ | Mean read quality: | 13.2 |
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+ | Median percent identity: | 87.3 |
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+ | Median read length: | 7577.0 |
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+ | Median read quality: | 13.5 |
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+ | Number of reads: | 1115 |
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+ | Read length N50: | 21987 |
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+ | Total bases: | 13704509 |
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+ | Total bases aligned: | 12343518 |
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+ | Number, percentage and megabases of reads above quality cutoffs |
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+ | >Q5: | 1115 (100.0%) 13.7Mb |
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+ | >Q7: | 1115 (100.0%) 13.7Mb |
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+ | >Q10: | 1098 (98.5%) 13.6Mb |
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+ | >Q12: | 936 (83.9%) 11.9Mb |
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+ | >Q15: | 10 (0.9%) 0.0Mb |
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+ | Top 5 highest mean basecall quality scores and their read lengths |
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+ | 1: | 15.7 (1461; SRR5665597.758) |
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+ | 2: | 15.5 (1790; SRR5665597.725) |
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+ | 3: | 15.5 (615; SRR5665597.293) |
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+ | 4: | 15.5 (162; SRR5665597.876) |
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+ | 5: | 15.5 (626; SRR5665597.822) |
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+ | Top 5 longest reads and their mean basecall quality score |
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+ | 1: | 99139 (13.9; SRR5665597.31) |
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+ | 2: | 80522 (13.5; SRR5665597.790) |
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+ | 3: | 79569 (13.5; SRR5665597.332) |
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+ | 4: | 70195 (10.2; SRR5665597.799) |
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+ | 5: | 69426 (12.2; SRR5665597.1000) |
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Summary statistics after filtering
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+ | General summary: |
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+ | Average percent identity: | 85.0 |
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+ | Mean read length: | 1436.3 |
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+ | Mean read quality: | 13.1 |
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+ | Median percent identity: | 86.8 |
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+ | Median read length: | 1419.5 |
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+ | Median read quality: | 13.4 |
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+ | Number of reads: | 80 |
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+ | Read length N50: | 1474 |
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+ | Total bases: | 114904 |
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+ | Total bases aligned: | 110215 |
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+ | Number, percentage and megabases of reads above quality cutoffs |
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+ | >Q5: | 80 (100.0%) 0.1Mb |
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+ | >Q7: | 80 (100.0%) 0.1Mb |
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+ | >Q10: | 77 (96.2%) 0.1Mb |
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+ | >Q12: | 64 (80.0%) 0.1Mb |
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+ | >Q15: | 3 (3.8%) 0.0Mb |
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+ | Top 5 highest mean basecall quality scores and their read lengths |
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+ | 1: | 15.7 (1461; SRR5665597.758) |
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+ | 2: | 15.5 (1790; SRR5665597.725) |
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+ | 3: | 15.1 (1474; SRR5665597.822) |
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+ | 4: | 14.7 (1985; SRR5665597.268) |
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+ | 5: | 14.6 (1726; SRR5665597.119) |
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+ | Top 5 longest reads and their mean basecall quality score |
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+ | 1: | 1985 (14.7; SRR5665597.268) |
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+ | 2: | 1981 (13.2; SRR5665597.912) |
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+ | 3: | 1969 (13.2; SRR5665597.827) |
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+ | 4: | 1955 (13.2; SRR5665597.213) |
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+ | 5: | 1930 (11.1; SRR5665597.21) |
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Plots
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Histogram of read lengths
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Weighted Histogram of read lengths
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Yield by length
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Read lengths vs Average read quality plot using dots
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Read lengths vs Average read quality plot using a kernel density estimation
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Aligned read lengths vs Sequenced read length plot using dots
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Aligned read lengths vs Sequenced read length plot using a kernel density estimation
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Read mapping quality vs Average basecall quality plot using dots
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Read mapping quality vs Average basecall quality plot using a kernel density estimation
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Read length vs Read mapping quality plot using dots
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Read length vs Read mapping quality plot using a kernel density estimation
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Percent identity vs Average Base Quality plot using dots
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Percent identity vs Average Base Quality plot using a kernel density estimation
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Aligned read length vs Percent identity plot using dots
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Aligned read length vs Percent identity plot using a kernel density estimation
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\ No newline at end of file
diff -r 000000000000 -r db1eeffba23e test-data/reads.fastq.gz
Binary file test-data/reads.fastq.gz has changed