---
name: "slurm_srst2"
section: "1"
platform: "linux"
package: "srst2"
version: "0.2.0-13"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/slurm_srst2"
---

# slurm\_srst2(1)

running srst2 against multiple read sets

## NAME

slurm\_srst2 - running srst2 against multiple read sets

## OPTIONS

**slurm\_srst2** \[**-h**\] \[**--walltime** WALLTIME\] \[**--memory** MEMORY\] \[**--rundir** RUNDIR\] **--script** SCRIPT **--output** OUTPUT \[**--input\_se** INPUT\_SE \[INPUT\_SE ...\]\] \[**--input\_pe** INPUT\_PE \[INPUT\_PE ...\]\] \[**--forward** FORWARD\] \[**--reverse** REVERSE\] \[**--other\_args** OTHER\_ARGS\]

## DESCRIPTION

Submit SRST2 jobs through SLURM (see srst(1))

## OPTIONS

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

  show this help message and exit

- **--walltime** WALLTIME

  wall time (default 0-1:0 = 1 h)

- **--memory** MEMORY

  mem (default 4096 = 4gb)

- **--rundir** RUNDIR

  directory to run in (default current dir)

- **--script** SCRIPT

  path to srst2 (default srst2)

- **--output** OUTPUT

  identifier for outputs (will be combined with read set identifiers)

- **--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)

- **--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)

- **--other\_args** OTHER\_ARGS

  string containing all other arguments to pass to srst2

## AUTHOR

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