seqkit.rst

Seqkit

Introduction ~~~~~~~~ Seqkit is a rapid tool for manipulating fasta and fastq files.

For more information, please check its website: https://biocontainers.pro/tools/seqkit and its home page on Github.

Versions

• 2.0.0
• 2.1.0
• 2.3.1

Commands ~~~~~~~ - seqkit

Module

You can load the modules by:

module load biocontainers
module load seqkit

Example job ~~~~~ .. warning:: Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Seqkit on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=seqkit
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers seqkit

seqkit stats configs.fasta > contigs_statistics.txt