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spades [2017/12/07 22:36] (current)
jokinsey Created documentation for spades
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 +====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.
 +
  
spades.txt · Last modified: 2017/12/07 22:36 by jokinsey