srst21

Usage

Overview

SRST2 - Short Read Sequence Typer (v2)

Options

-h, --help

show this help message and exit

--version

show program's version number and exit

--merge_paired

Switch on if all the input read sets belong to a single sample, and you want to merge their data to get a single result

--forward FORWARD

Designator for forward reads (only used if NOT in MiSeq format sample_S1_L001_R1_001.fastq.gz; otherwise default is _1, i.e. expect forward reads as sample_1.fastq.gz)

--reverse REVERSE

Designator for reverse reads (only used if NOT in MiSeq format sample_S1_L001_R2_001.fastq.gz; otherwise default is _2, i.e. expect forward reads as sample_2.fastq.gz

--read_type {q,qseq,f}

Read file type (for bowtie2; default is q=fastq; other options: qseq=solexa, f=fasta).

--mlst_db MLST_DB

Fasta file of MLST alleles (optional)

--mlst_delimiter MLST_DELIMITER

Character(s) separating gene name from allele number in MLST database (default "-", as in arcc-1)

--mlst_definitions MLST_DEFINITIONS

ST definitions for MLST scheme (required if mlst_db supplied and you want to calculate STs)

--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

Switch OFF verbose reporting of gene typing

--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 dubious allele call (default 5)

--min_edge_depth MIN_EDGE_DEPTH

Minimum edge depth to flag as 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 map all)

--other OTHER

Other arguments to pass to bowtie2 (must be escaped, e.g. "\--no-mixed".

--mapq MAPQ

Samtools -q parameter (default 1)

--baseq BASEQ

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 srst2 output files

--log

Switch ON logging to file (otherwise log to stdout)

--save_scores

Switch ON verbose reporting of all scores

--report_new_consensus

If a matching alleles 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, only SNP differences are considered, not indels.

--use_existing_pileup

Use existing pileups if available, otherwise they will be generated

--use_existing_scores

Use existing scores files if available, otherwise they will be generated

--keep_interim_alignment

Keep interim files (sam & unsorted bam), otherwise they will be deleted after sorted bam is created

--prev_output PREV_OUTPUT [PREV_OUTPUT ...]

SRST2 results files to compile (any new results from this run will also be incorporated)

Examples

Assume you have a database 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

Looks like --mlst_delimiter '-'

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

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