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Question: bioconductor package for BWA-MEM ?
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gravatar for K
2.3 years ago by
K40
United States
K40 wrote:

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,

ADD COMMENTlink modified 2.3 years ago by Gordon Smyth32k • written 2.3 years ago by K40
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gravatar for Gordon Smyth
2.3 years ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

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 COMMENTlink modified 2.3 years ago • written 2.3 years ago by Gordon Smyth32k

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

ADD REPLYlink written 2.3 years ago by K40

There is also gmapR, too ;-)

ADD REPLYlink written 2.3 years ago by Steve Lianoglou12k
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 REPLYlink modified 2.3 years ago by Dan Tenenbaum ♦♦ 8.2k • written 2.3 years ago by Thomas Girke1.6k

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

ADD REPLYlink written 2.3 years ago by K40
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