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abyss [2017/11/07 23:53] (current)
jokinsey Create abyss documentation
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 +====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>​
 +
 +
 +
 +
 +
  
abyss.txt · Last modified: 2017/11/07 23:53 by jokinsey