Using the BWA-mem aligner

The BWA-mem aligner is one of a series of alignment functions found in the BWA aligner. It is well adapted to accurate mapping of longer sequences to genome. The app runs on the Stampede server, part of the XSEDE system of supercomputers. Speed and accessible memory is high for this app. The app runs an indexing step before performing the alignment in order to create an index of the genome sequence to use for mapping.

Step-by-step guide for Sample Data

Files are entered as a directory. For the sample data use BAcon1 ( Community Data > iplantcollaborative > example_data > bwa-mem > inputs > BAcon1 ), which contains 2 paired sequence files. Use BAgenomeRay41.fa as the reference sequence. Set paired vs unpaired to paired. Leave all other settings to default.

 

The output files are in the outputs directory in the sample data section ( Community Data > iplantcollaborative > example_data > bwa-mem > inputs > BWA_output, Community Data > iplantcollaborative > example_data > bwa-mem > inputs > BWA_output_BAM ).

 

http://research-pub.gene.com/gmap/

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