spades
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spades [2017/12/07 22:36] (current) jokinsey Created documentation for spades |
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| + | ====Spades==== | ||
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| + | 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
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