====Velvet====

Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom. You can find out more about Velvet [[https://www.ebi.ac.uk/~zerbino/velvet/|here]].

====Environment Setup====

To use Velvet first we will have to load the velvet module. You can do this by adding this line to your '.bashrc' file.

<code>
module load velvet
</code>

Before you run your code you'll want to create a directory to store the files as shown below.

<code>
razor-l1:jokinsey:~$ mkdir VELVET-TEST
razor-l1:jokinsey:~$ cd VELVET-TEST/
razor-l1:jokinsey:~/VELVET-TEST$ cp /share/apps/velvet/velvet_1.2.10/data/test_reads.fa .
</code>

====Example Job====

Now that we have our input file 'test_reads.fa', create a PBS script to run the job named 'velvet.pbs' that has the information below.

<code>
#!/bin/bash
#PBS -N velvet
#PBs -o velvet.$PBS_JOBID
#PBS -l nodes=1:ppn=12
#PBS -l walltime=00:05:00
#PBS -q tiny12core

cd $PBS_O_WORKDIR
cp test_reads.fa /scratch/$PBS_JOBID
cd /scratch/$PBS_JOBID

velveth velvet1 29 test_reads.fa
velvetg velvet1
mv velvet1 $PBS_O_WORKDIR
</code>

This code will copy the test file to the ''/scratch/$PBS_JOBID'' directory where we will be submitting the job from. Then the output will be in the directory ''velvet1'' which we move back to the directory we submitted the job from. Note that if you have already run the script you will have to remove the previous ''velvet1'' directory for the move command to work.

All that remains is to submit the job.

<code>
razor-l1:jokinsey:~/VELVET-TEST$ qsub velvet.pbs
</code> 

The most important output files will be '/velvet1/configs.fa', '/velvet1/Graph', and '/velvet1/stats.txt'.