Velvet

Introduction

Velvet is a sequence assembler for very short reads.

For more information, please check its website: https://biocontainers.pro/tools/velvet and its home page: https://www.ebi.ac.uk/~zerbino/velvet/.

Versions

1.2.10

Commands

velveth
velvetg

Module

You can load the modules by:

module load biocontainers
module load trimmomatic

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 Velvet on our clusters:

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

module --force purge
ml biocontainers velvet

velveth output_directory 21 -fasta -short solexa1.fa solexa2.fa solexa3.fa -long capillary.fa
velvetg output_directory -cov_cutoff 4