Index of /examples/bioinformatics/spades

Icon  Name                    Last modified      Size  Description
[DIR] Parent Directory - [   ] spades_job.qsub 08-Mar-2015 21:28 333 [DIR] test_dataset/ 08-Mar-2015 21:24 - [DIR] spades_test/ 08-Mar-2015 21:26 -

SPAdes package example

To run SPAdes at the command line:

scc4% module load spades/3.5.0

scc4% spades.py -h

scc4% spades.py --pe1-1 test_dataset/ecoli_1K_1.fq.gz --pe1-2 test_dataset/ecoli_1K_2.fq.gz -o spades_test

To submit a job, execute command:
scc4% qsub -P my_project spades_job.qsub

Manual for the software, can be found here:
http://spades.bioinf.spbau.ru/release3.5.0/manual.html