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Velvet

Velvet is a sequence assembler for very short reads.

License

Free to use and open source under GNU GPLv2.

Available

  • Puhti: 1.2.10
  • Chipster graphical user interface

Usage

On Puhti, the Velvet commands are initialized with the command:

module load biokit

velveth (and the corresponding colorspace version velveth_de) helps you construct the dataset for the velvetg program. Velveth takes in a number of sequence files, produces a hashtable, then outputs two files in an output directory, Sequences and Roadmaps, which are necessary to Velvetg. The syntax is as follows:

velveth output_directory hash_length  [[-file_format][-read_type] filename]

For example:

velveth assembly_dir 21 -shortPaired data/reads.fa

velvetg (and the corresponding colorspace version velvetg_de) is the core of Velvet where the de Bruijn graph is built and then manipulated. The syntax of velvetg is:

velvetg output_directory -options parameters

A velvetg command could look like:

velvetg assembly_dir -cov_cutoff 5 -read_trkg yes -amos_file yes

When Velvet was compiled on Puhti, the maximum allowed k-mer length was defined. The longer the maximum k-mer is, the more memory Velvet will need (regardless of the k-mer length that is actually used). Because of that we provide several versions of Velvet, listed in the table below. On Puhti, the default maximum k-mer length that can be used in the hash table is 100 bases. However, it is recommended to use the version that has the shortest possible max k-mer length. For example, for k-mer length 40, you should use velveth_maxk50 and velvetg_maxk50.

Velvet programs available on Puhti

Program max. k-mer length type
velveth 100 normal
velvetg 100 normal
velveth_maxk75 75 normal
velvetg_maxk75 75 normal
velveth_maxk50 50 normal
velvetg_maxk50 50 normal
velveth_maxk35 35 normal
velvetg_maxk35 35 normal
velveth_de 100 colorspace
velvetg_de 100 colorspace
velveth_de_maxk75 75 colorspace
velvetg_de_maxk75 75 colorspace
velveth_de_maxk50 50 colorspace
velvetg_de_maxk50 50 colorspace
velveth_de_maxk35 35 colorspace
velvetg_de_maxk35 35 colorspace

On Puhti, the Velvet jobs should be executed through the batch job system. Below is sample batch job file for Velvet:

#!/bin/bash
#SBATCH --job-name=velvet
#SBATCH --output=put=output_velvet2.txt
#SBATCH --error=errors_velvet2.txt
#SBATCH --account=<project>
#SBATCH --time=4-00:00:00
#SBATCH --ntasks=1
#SBATCH --partition=longrun
#SBATCH --nodes=1
#SBATCH --cpus-per-task=4
#SBATCH --mem=64G

module load biokit
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK
export OMP_THREAD_LIMIT=$SLURM_CPUS_PER_TASK

velveth_maxk50 assembly_folder 45 -shortPaired -fastq temp.fastq
velvetg_maxk50 assembly_folder -ins_length 400

In the batch job file above, the job reserves 4 computing cores (--cpus-per-task=4) and 64 GB of memory for four days (--time=4-00:00:00). Velvet can utilize thread-based parallel computing. After the setup command module load biokit, the number of cores to be used in the Velvet run is defined with the environment variables $OMP_NUM_THREADS and $OMP_THREAD_LIMIT. In this script these variables are set by using the environment variable $SLURM_CPUS_PER_TASK that contains the value defined with --cpus-per-task (which, in this example, has the value 4).

The batch job can be launched with the command:

sbatch script_file_name

More information about running batch jobs can be found from the batch job section of the Puhti user guide.

More information

More information about Velvet can be found from: