Vsearch
Introduction
Vsearch
is a versatile open source tool for metagenomics.
For more information, please check its website: https://biocontainers.pro/tools/vsearch and its home page on Github.
Versions
2.19.0
2.21.1
2.22.1
Commands
vsearch
Module
You can load the modules by:
module load biocontainers
module load vsearch
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 Vsearch on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=vsearch
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers vsearch
vsearch -sintax SRR8723605_merged.fasta -db rdp_16s_v16_sp.fa \
-tabbedout SRR8723605_out.txt -strand both -sintax_cutoff 0.5