====Abyss====

ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. You can fins more information on abyss [[http://www.bcgsc.ca/platform/bioinfo/software/abyss|here]].

====Environment Setup====

To work with abyss first we need to load abyss and it's dependencies. The easiest way to do this is to modify the ''.bashrc'' file in your ''$HOME'' directory.

<code>
module load gcc
module load mpi
module load openmpi
module load intel/13.1.0
module load abyss/2.0.2
</code>

Create a directory in your ''$HOME'' directory where you can submit and run the example job. Copy the ''fastaq'' files used for the example job from the examples directory located with the abyss software.

<code>
razor-l1:jokinsey:~$ mkdir ABYSS-JOBS
razor-l1:jokinsey:~$ cp /share/apps/abyss/examples/SRR001665_* ABYSS-JOBS/
</code>

====Example Job====

To run the example job create a ''PBS'' script file with the information below that we can submit to run the job.

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

cd $PBS_O_WORKDIR
cp SRR001665_1.fastq  SRR001665_2.fastq /scratch/$PBS_JOBID

cd /scratch/$PBS_JOBID

abyss-pe mpirun='mpirun -v -machinefile $(PBS_NODEFILE)' name=ecoli k=31 in='SRR001665_1.fastq  SRR001665_2.fastq'
mkdir $PBS_O_WORKDIR/abyss.$PBS_JOBID
cd $PBS_O_WORKDIR/abyss.$PBS_JOBID
cp -r /scratch/$PBS_JOBID/* 
</code>

This script will produce a directory with the output in the submission directory. You can find information on the output [[https://github.com/bcgsc/abyss#abyss|here]].

Alls thats left to do is submit the job.

<code>
razor-l1:jokinsey:~/ABYSS-JOBS$ qsub abyss.pbs 
</code>

Once you have your output for this given example try running the command below on the file ''ecoli-1.fa'' and verify your output.

<code>
razor-l1:jokinsey:~/ABYSS-JOBS/abyss.3539296.sched$ abyss-fac ecoli-1.fa 
n	n:500	L50	min	N80	N50	N20	E-size	max	sum	name
1833	414	71	518	8892	18242	36985	23425	67081	4512653	ecoli-1.fa
</code>