====Spades====

SPAdes – St. Petersburg genome assembler – is an assembly toolkit containing various assembly pipelines. You can find more information on SPAdes [[http://cab.spbu.ru/software/spades/|here]].

====Environment Setup====

To use spades edit your ''$HOME/.bashrc'' to include the spades module.

<code>
module load spades
</code>

Create a folder in your ''$HOME'' directory that you will submit the jobs from. 

<code>
razor-l1:jokinsey:~$ mkdir SPADES-JOBS
razor-l1:jokinsey:~$ cd SPADES-JOBS/
</code>

Copy the example files for the test from the spades documentation.

<code>
razor-l1:jokinsey:~$ cp /share/apps/spades/SPAdes-3.6.0/test_dataset/ecoli_1K_* .
</code>

====Example====

Create a ''PBS'' file that will run the test job, which looks like the one below.

<code>
#!/bin/bash
#PBS -N spades
#PBS -q tiny12core
#PBS -j oe
#PBS -o spades.$PBS_JOBID
#PBS -l nodes=1:ppn=12
#PBS -l walltime=0:05:00

cd $PBS_O_WORKDIR
cp ecoli_1K_* /scratch/$PBS_JOBID
cd /scratch/$PBS_JOBID

spades.py --pe1-1 ecoli_1K_1.fq.gz --pe1-2 ecoli_1K_2.fq.gz -o spades_test

mkdir $PBS_O_WORKDIR/spades.$PBS_JOBID
cd $PBS_O_WORKDIR/$PBS_JOBID
cp -r /scratch/$PBS_JOBID/* .
</code>

You can find more information on the commands being run [[http://spades.bioinf.spbau.ru/release3.11.1/manual.html#sec3.2|here]].

All thats left to do is submit the job.

<code>
razor-l1:jokinsey:~/SPADES-JOBS$ qsub spades.pbs 
</code>

The important output will be in the directory ''$HOME/SPADES-JOBS/spades.$PBS_JOBID/spades_test/'', a good place to start would be the file ''spades.log'' in that given directory.