---
name: "srst2"
section: "1"
platform: "linux"
package: "srst2"
version: "0.2.0-13"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/srst2"
---

# srst2(1)

Short Read Sequence Typer

## NAME

srst2 - Short Read Sequence Typer

## 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 \[PREV\_OUTPUT ...\]\]

## DESCRIPTION

SRST2 - Short Read Sequence Typer (v2)

## OPTIONS

- **-h**, **--help**

  show this help message and exit

- **--version**

  show program's version number and exit

- **--input\_se** INPUT\_SE \[INPUT\_SE ...\]

  Single end read file(s) for analysing (may be gzipped)

- **--input\_pe** INPUT\_PE \[INPUT\_PE ...\]

  Paired end read files for analysing (may be gzipped)

- **--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)

## EXAMPLE

Assume you have a database downloaded by [getmlst(1)](/getmlst/1.md) 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

## 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.