Question

bioconductor package for BWA-MEM ?

0

Entering edit mode

KB ▴ 50

@k-8495

Last seen 15 months ago

United States

Hello,

I was wondering if there is a R/Bioconductor package that can run BWA-mem alignment (just like how RSamtools is the Bioconductor implementation of Samtools).

I am looking to consolidate all my analyses in R/Bioconductor, instead of having half my things in unix and other parts in R.

Thanks,

bwa ngs • 4.6k views

ADD COMMENT • link updated 8.7 years ago by Gordon Smyth 50k • written 8.7 years ago by KB ▴ 50

Dan Tenenbaum · Answer 1 · 2015-08-12

0

Entering edit mode

Gordon Smyth 50k

@gordon-smyth

Last seen 5 hours ago

WEHI, Melbourne, Australia

See the BiocViews page for "alignment":

http://www.bioconductor.org/packages/release/BiocViews.html#___Alignment

As far as I know, there is no Bioconductor implementation of BWA.

The Rsubread package provides a native implementation of the subread aligner.

The QuasR and Rbowtie packages provide R wrappers for the bowtie and SpliceMap aligners.

ADD COMMENT • link 8.7 years ago Gordon Smyth 50k

0

Entering edit mode

Thanks for the response. I will go through the packages you suggested.

ADD REPLY • link 8.7 years ago KB ▴ 50

0

Entering edit mode

There is also gmapR, too ;-)

ADD REPLY • link 8.7 years ago Steve Lianoglou ★ 13k

0

Entering edit mode

Also, if the variant tolerance of BWA is important to you then the gsnap aligner from the gmapR package might be a great alternative. If you need BWA directly and you don't mind using a system command-based interface then the systemPipeR package might provide some solutions. The main and VAR-Seq vignettes give some examples how to run bwa mem. Thomas

ADD REPLY • link updated 8.7 years ago by Dan Tenenbaum ★ 8.2k • written 8.7 years ago by Thomas Girke ★ 1.7k

0

Entering edit mode

Thanks ! The systemPipeR might be exactly what I am looking for...I will definitely try this out. Thanks for all the suggestions.

ADD REPLY • link 8.7 years ago KB ▴ 50