ss2v110: README.md annotate

annotate README.md @ 13:e3b74e412f40 draft

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author	cstrittmatter
date	Fri, 15 May 2020 10:37:52 -0400
parents	e6437d423693
children

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10 e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	1 # SeqSero2 v1.1.1
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	2 Salmonella serotype prediction from genome sequencing data.
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	3
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	4 Online version: http://www.denglab.info/SeqSero2
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e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	6 # Introduction
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	7 SeqSero2 is a pipeline for Salmonella serotype prediction from raw sequencing reads or genome assemblies
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10 e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	9 # Dependencies
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	10 SeqSero2 has three workflows:
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e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	12 (A) Allele micro-assembly (default). This workflow takes raw reads as input and performs targeted assembly of serotype determinant alleles. Assembled alleles are used to predict serotype and flag potential inter-serotype contamination in sequencing data (i.e., presence of reads from multiple serotypes due to, for example, cross or carryover contamination during sequencing).
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10 e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	14 Allele micro-assembly workflow depends on:
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e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	16 1. Python 3;
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	17
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	18 2. Biopython 1.73;
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	19
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	20 3. [Burrows-Wheeler Aligner v0.7.12](http://sourceforge.net/projects/bio-bwa/files/);
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10 e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	22 4. [Samtools v1.8](http://sourceforge.net/projects/samtools/files/samtools/);
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e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	24 5. [NCBI BLAST v2.2.28+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download);
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e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	26 6. [SRA Toolkit v2.8.0](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software);
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e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	28 7. [SPAdes v3.9.0](http://bioinf.spbau.ru/spades);
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e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	30 8. [Bedtools v2.17.0](http://bedtools.readthedocs.io/en/latest/);
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10 e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	32 9. [SalmID v0.11](https://github.com/hcdenbakker/SalmID).
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e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	34
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	35 (B) Raw reads k-mer. This workflow takes raw reads as input and performs rapid serotype prediction based on unique k-mers of serotype determinants.
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10 e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	37 Raw reads k-mer workflow (originally SeqSeroK) depends on:
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10 e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	39 1. Python 3;
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	40 2. [SRA Toolkit](http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software) (optional, just used to fastq-dump sra files);
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	41
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	42
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	43 (C) Genome assembly k-mer. This workflow takes genome assemblies as input and the rest of the workflow largely overlaps with the raw reads k-mer workflow
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10 e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	45 # Installation
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	46 ### Conda
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	47 To install the latest SeqSero2 Conda package (recommended):
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	48 ```
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	49 conda install -c bioconda seqsero2=1.1.1
2 d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: 0 diff changeset	50 ```
10 e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	51 ### Git
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	52 To install the SeqSero2 git repository locally:
2 d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: 0 diff changeset	53 ```
10 e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	54 git clone https://github.com/denglab/SeqSero2.git
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	55 cd SeqSero2
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	56 python3 -m pip install --user .
2 d0350fe29fdf planemo upload commit c50df40caef2fb97c178d6890961e0e527992324 cstrittmatter parents: 0 diff changeset	57 ```
10 e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	58 ### Other options
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	59 Third party SeqSero2 installations (may not be the latest version of SeqSero2): \
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	60 https://github.com/B-UMMI/docker-images/tree/master/seqsero2 \
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	61 https://github.com/denglab/SeqSero2/issues/13
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e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	63
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	64 # Executing the code
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	65 Make sure all SeqSero2 and its dependency executables are added to your path (e.g. to ~/.bashrc). Then type SeqSero2_package.py to get detailed instructions.
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e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	67 Usage: SeqSero2_package.py
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	68
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	69 -m <string> (which workflow to apply, 'a'(raw reads allele micro-assembly), 'k'(raw reads and genome assembly k-mer), default=a)
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e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	71 -t <string> (input data type, '1' for interleaved paired-end reads, '2' for separated paired-end reads, '3' for single reads, '4' for genome assembly, '5' for nanopore fasta, '6'for nanopore fastq)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	72
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	73 -i <file> (/path/to/input/file)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	74
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	75 -p <int> (number of threads for allele mode, if p >4, only 4 threads will be used for assembly since the amount of extracted reads is small, default=1)
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10 e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	77 -b <string> (algorithms for bwa mapping for allele mode; 'mem' for mem, 'sam' for samse/sampe; default=mem; optional; for now we only optimized for default "mem" mode)
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e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	79 -d <string> (output directory name, if not set, the output directory would be 'SeqSero_result_'+time stamp+one random number)
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e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	81 -c <flag> (if '-c' was flagged, SeqSero2 will only output serotype prediction without the directory containing log files)
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e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	83 -n <string> (optional, to specify a sample name in the report output)
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e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	85 -s <flag> (if '-s' was flagged, SeqSero2 will not output header in SeqSero_result.tsv)
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e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	87 --check <flag> (use '--check' flag to check the required dependencies)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	88
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	89 -v, --version (show program's version number and exit)
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	90
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	91
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	92 # Examples
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	93 Allele mode:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	94
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	95 # Allele workflow ("-m a", default), for separated paired-end raw reads ("-t 2"), use 10 threads in mapping and assembly ("-p 10")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	96 SeqSero2_package.py -p 10 -t 2 -i R1.fastq.gz R2.fastq.gz
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e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	98 K-mer mode:
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	99
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	100 # Raw reads k-mer ("-m k"), for separated paired-end raw reads ("-t 2")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	101 SeqSero2_package.py -m k -t 2 -i R1.fastq.gz R2.fastq.gz
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e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	103 # Genome assembly k-mer ("-t 4", genome assemblies only predicted by the k-mer workflow, "-m k")
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	104 SeqSero2_package.py -m k -t 4 -i assembly.fasta
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	105
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	106 # Output
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	107 Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using "-m a" (allele mode).
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	108
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	109
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	110 # Citation
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	111 Zhang S, Den-Bakker HC, Li S, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X.
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	112 SeqSero2: rapid and improved Salmonella serotype determination using whole genome sequencing data.
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	113 Appl Environ Microbiology. 2019 Sep; 85(23):e01746-19. [PMID: 31540993](https://aem.asm.org/content/early/2019/09/17/AEM.01746-19.long)
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e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	115 Zhang S, Yin Y, Jones MB, Zhang Z, Deatherage Kaiser BL, Dinsmore BA, Fitzgerald C, Fields PI, Deng X.
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	116 Salmonella serotype determination utilizing high-throughput genome sequencing data.
e6437d423693 planemo upload commit 70dc513aa7d7ac6785847dfd86323687613b6b68-dirty cstrittmatter parents: 2 diff changeset	117 J Clin Microbiol. 2015 May;53(5):1685-92. [PMID: 25762776](http://jcm.asm.org/content/early/2015/03/05/JCM.00323-15)

Mercurial > repos > cstrittmatter > ss2v110

annotate README.md @ 13:e3b74e412f40 draft