Table of Contents
Abyss
ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. You can fins more information on 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.
module load gcc module load mpi module load openmpi module load intel/13.1.0 module load abyss/2.0.2
Create a directory in your $HOME directory where you can submit and run the example job. Copy the fastaq files used for the example job from the examples directory located with the abyss software.
razor-l1:jokinsey:~$ mkdir ABYSS-JOBS razor-l1:jokinsey:~$ cp /share/apps/abyss/examples/SRR001665_* ABYSS-JOBS/
Example Job
To run the example job create a PBS script file with the information below that we can submit to run the job.
#!/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/$PBS_JOBID/*
This script will produce a directory with the output in the submission directory. You can find information on the output here.
Alls thats left to do is submit the job.
razor-l1:jokinsey:~/ABYSS-JOBS$ qsub abyss.pbs
Once you have your output for this given example try running the command below on the file ecoli-1.fa and verify your output.
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
