Index of /examples/bioinformatics/bwa

Icon  Name                    Last modified      Size  Description
[DIR] Parent Directory - [   ] chr2R.fa 08-Mar-2015 19:21 21M [   ] bwa_job.qsub 08-Mar-2015 19:27 249

BWA package example

To run BWA at the command line:

scc4% module load bwa/0.7.12

scc4% bwa index chr2R.fa
[bwa_index] Pack FASTA... 0.28 sec
[bwa_index] Construct BWT for the packed sequence...
[bwa_index] 16.02 seconds elapse.
[bwa_index] Update BWT... 0.15 sec
[bwa_index] Pack forward-only FASTA... 0.18 sec
[bwa_index] Construct SA from BWT and Occ... 4.22 sec
[main] Version: 0.7.12-r1039
[main] CMD: bwa index chr2R.fa
[main] Real time: 20.963 sec; CPU: 20.862 sec

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

Manual for BWA: