SeqKit
SeqKit is a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. It provides a wide range of subcommands for common sequence operations such as statistics, searching, filtering, subsampling and format conversion.
License
Free to use and open source under the MIT License.
Available
- Roihu-CPU: 2.10.0, 2.13.0, via the
bio-appsmodule.
Usage
SeqKit is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the SeqKit module:
SeqKit is run through the seqkit command followed by a subcommand. For example, to
print summary statistics for a set of FASTA files:
or to filter sequences by minimum length:
Example batch script
#!/bin/bash
#SBATCH --job-name=seqkit
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=2G
module load bio-apps/v202603
module load seqkit/2.13.0
seqkit stats -j $SLURM_CPUS_PER_TASK *.fasta
Replace <project> with your CSC project (for example project_2001234).
See creating a batch job script for Roihu for more information about running batch jobs.