The first step of running Velvet is to run velveth:
velveth.submit
#!/bin/bash
#SBATCH --job-name=Velvet_Velveth
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --time=168:00:00
#SBATCH --mem=10gb
#SBATCH --output=Velveth.%J.out
#SBATCH --error=Velveth.%J.err
module load velvet/1.2
export OMP_NUM_THREADS=$SLURM_NTASKS_PER_NODE
velveth output_directory/ 51 -fasta -short input_reads.fasta -fasta -shortPaired2 -separate input_reads_pair_1.fasta input_reads_pair_2.fasta
After running velveth, the next step is to run velvetg on the output_directory/
and files generated from velveth:
velvetg.submit
#!/bin/bash
#SBATCH --job-name=Velvet_Velvetg
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=8
#SBATCH --time=168:00:00
#SBATCH --mem=100gb
#SBATCH --output=Velvetg.%J.out
#SBATCH --error=Velvetg.%J.err
module load velvet/1.2
export OMP_NUM_THREADS=$SLURM_NTASKS_PER_NODE
velvetg output_directory/ -min_contig_lgth 200
Both velveth and velvetg are multi-threaded.
Output directory after velveth
$ ls output_directory/
Log Roadmaps Sequences
Output directory after velvetg
$ ls output_directory/
contigs.fa Graph LastGraph Log PreGraph Roadmaps Sequences stats.txt
The output fasta file contigs.fa
is the final Velvet output that contains the assembled contigs. More information about the output files is provided in the Velvet manual.