SRST2(1)

💖 srst2 — Short Read Sequence Typer 💖

okay bestie, pull up a chair, we're doing SRST2 today (that's section 1 of the manual, SRST2(1) if you're keeping score) and honestly? it's giving short read sequence typer and it is SO much less scary than it sounds. let's go 💅

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✨ SYNOPSIS ✨

srst2 [-h] [--version] [--input_se INPUT_SE [INPUT_SE ...]] [--input_pe
INPUT_PE [INPUT_PE ...]] [--merge_paired] [--forward FORWARD] [--reverse
REVERSE] [--read_type {q,qseq,f}] [--mlst_db MLST_DB] [--mlst_delimiter
MLST_DELIMITER] [--mlst_definitions MLST_DEFINITIONS]
[--mlst_max_mismatch MLST_MAX_MISMATCH] [--gene_db GENE_DB [GENE_DB
...]] [--no_gene_details] [--gene_max_mismatch GENE_MAX_MISMATCH]
[--min_coverage MIN_COVERAGE] [--max_divergence MAX_DIVERGENCE]
[--min_depth MIN_DEPTH] [--min_edge_depth MIN_EDGE_DEPTH] [--prob_err
PROB_ERR] [--stop_after STOP_AFTER] [--other OTHER] [--mapq MAPQ]
[--baseq BASEQ] [--samtools_args SAMTOOLS_ARGS] --output OUTPUT [--log]
[--save_scores] [--report_new_consensus] [--report_all_consensus]
[--use_existing_pileup] [--use_existing_scores]
[--keep_interim_alignment] [--prev_output PREV_OUTPUT [PREV_OUTPUT ...]]

like yes it's a lot of brackets, breathe, we'll get to every single one 🫶

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🌸 DESCRIPTION 🌸

SRST2 - Short Read Sequence Typer (v2)

that's the whole description. short. sweet. main character energy honestly. it types your short reads. it's the whole vibe. 👑

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🎀 OPTIONS 🎀

one bullet per flag, no skipping, we're thorough in this house:

• -h, --help — shows you this help message and then dips. classic. ✨
• --version — prints the program's version number and exits. little flex. 💅
• --input_se INPUT_SE [INPUT_SE ...] — single end read file(s) to analyse. yes bestie, they may be gzipped. 🍓
• --input_pe INPUT_PE [INPUT_PE ...] — paired end read files for analysing. also may be gzipped, we love a flexible queen. 🦋
• --merge_paired — turn this ON if all your input read sets belong to a single sample and you want to merge their data so you get one single result. one sample, one result, one vibe. 💜
• --forward FORWARD — the designator for forward reads. heads up: this is only used if you're NOT in MiSeq format sample_S1_L001_R1_001.fastq.gz — otherwise the default is _1, i.e. it expects forward reads as sample_1.fastq.gz.
• --reverse REVERSE — the designator for reverse reads. same deal: only used if you're NOT in MiSeq format sample_S1_L001_R2_001.fastq.gz — otherwise the default is _2, i.e. it expects forward reads as sample_2.fastq.gz. (yes, the original says "forward reads" there for the reverse option, we are simply reporting the lore as written, no cap 🙈)
• --read_type {q,qseq,f} — read file type, for bowtie2. default is q = fastq. other options: qseq = solexa, f = fasta. pick your fighter. 🌈
• --mlst_db MLST_DB — fasta file of MLST alleles. it's optional, but like… you probably want it. ✨
• --mlst_delimiter MLST_DELIMITER — the character(s) separating gene name from allele number in the MLST database. default is "-", as in arcc-1. iconic little hyphen. 🎀
• --mlst_definitions MLST_DEFINITIONS — ST definitions for the MLST scheme. required if mlst_db is supplied and you actually want to calculate STs. no definitions, no STs, that's the deal. 💀
• --mlst_max_mismatch MLST_MAX_MISMATCH — maximum number of mismatches per read for MLST allele calling. default 10.
• --gene_db GENE_DB [GENE_DB ...] — fasta file/s for gene databases. optional. 🌸
• --no_gene_details — switches OFF verbose reporting of gene typing. shy mode. 🙈
• --gene_max_mismatch GENE_MAX_MISMATCH — maximum number of mismatches per read for gene detection and allele calling. default 10.
• --min_coverage MIN_COVERAGE — minimum %coverage cutoff for gene reporting. default 90.
• --max_divergence MAX_DIVERGENCE — maximum %divergence cutoff for gene reporting. default 10.
• --min_depth MIN_DEPTH — minimum mean depth to flag as a dubious allele call. default 5.
• --min_edge_depth MIN_EDGE_DEPTH — minimum edge depth to flag as a dubious allele call. default 2.
• --prob_err PROB_ERR — probability of sequencing error. default 0.01.
• --stop_after STOP_AFTER — stop mapping after this number of reads have been mapped. otherwise it maps all of them. (all. every last one. 😭)
• --other OTHER — other arguments to pass to bowtie2. must be escaped, e.g. "\--no-mixed".
• --mapq MAPQ — the samtools -q parameter. default 1.
• --baseq BASEQ — the samtools -Q parameter. default 20.
• --samtools_args SAMTOOLS_ARGS — other arguments to pass to samtools mpileup. must be escaped, e.g. "\-A".
• --output OUTPUT — prefix for the srst2 output files. this one's required, note there's no brackets around it in the synopsis. periodt. 👑
• --log — switch ON logging to file. otherwise it logs to stdout. 🌟
• --save_scores — switch ON verbose reporting of all scores. 💅
• --report_new_consensus — if a matching allele is not found, report the consensus allele. note: only SNP differences are considered, not indels. 💖
• --report_all_consensus — report the consensus allele for the most likely allele. note: again, only SNP differences are considered, not indels. 🦋
• --use_existing_pileup — use existing pileups if they're available. otherwise they will be generated. 🎀
• --use_existing_scores — use existing scores files if available. otherwise they will be generated. ✨
• --keep_interim_alignment — keep the interim files (sam & unsorted bam). otherwise they get deleted after the sorted bam is created. RIP little files. 💀
• --prev_output PREV_OUTPUT [PREV_OUTPUT ...] — SRST2 results files to compile. any new results from this run will also be incorporated. 🌈

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🌟 EXAMPLE 🌟

okay so imagine you've got a database that was downloaded by getmlst(1) by using:

getmlst --species "Escherichia coli#1"

for SRST2, remember to check what separator is being used in this allele database bestie, do not skip this step. 🔍

looks like --mlst_delimiter '-'

>adk-1  --> -->   ('adk', '-', '1')

and the suggested srst2 command for use with this MLST database:

srst2 --output test --input_pe *.fastq.gz --mlst_db
Escherichia_coli#1.fasta --mlst_definitions ecoli.txt
--mlst_delimiter '-'

note: this is correctly guessing that we should use the default --mlst_delimiter '-' with this database. the log file will tell you exactly what files were downloaded. 📝

more verbose example usage is described in /usr/share/doc/srst2/example.txt.gz. go read it, it's a whole thing. 🫶

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💜 AUTHOR 💜

• Michael Inouye (minouye@unimelb.edu.au)
• Harriet Dashnow (h.dashnow@gmail.com)
• Kathryn Holt (kholt@unimelb.edu.au)
• Bernie Pope (bjpope@unimelb.edu.au)

this manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. 💖

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and that's the whole page bestie!! srst2 0.1.6, dated December 2015 — go type some reads, you're gonna slay. mwah 💅✨🎀