Running Velvet with Single-End and Paired-End Data

Running Velvet with Single-End and Paired-End short fasta data with k-mer=51, 8 CPUs and 100GB of RAM

The first step of running Velvet is to run velveth:

velveth.submit
#!/bin/sh
#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/sh
#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.

Velvet Output

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.