Question

bioconductor package for BWA-MEM ?

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@k-8495

Last seen 23 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 • 5.0k views

ADD COMMENT • link updated 9.3 years ago by Gordon Smyth 52k • written 9.3 years ago by KB ▴ 50

Dan Tenenbaum · Answer 1 · 2015-08-12

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Gordon Smyth 52k

@gordon-smyth

Last seen 2 minutes 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 9.3 years ago Gordon Smyth 52k

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

ADD REPLY • link 9.3 years ago KB ▴ 50

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There is also gmapR, too ;-)

ADD REPLY • link 9.3 years ago Steve Lianoglou ★ 13k

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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 9.3 years ago by Dan Tenenbaum ★ 8.2k • written 9.3 years ago by Thomas Girke ★ 1.7k

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

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