Question: Rsubread versus BWA ( Burrows-Wheeler Alignmener) for whole genome alignment
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gravatar for tarek.mohamed
4.2 years ago by
tarek.mohamed270
tarek.mohamed270 wrote:

Hi All,

I have some whole genome sequencing data that were generated from illumina hiseq platform.

as a first step, I will align the fastq file to a reference genome. Can I use Rsubread for that? I have used it for RNAseq mapping before and it was very good, I got 90% of the read were mapped to the ref genome. Does BWA have any advantage as compared to Rsubread.

Thanks

Tarek

bwa rsubread ngs • 1.4k views
ADD COMMENTlink modified 20 months ago by Gordon Smyth2.0k • written 4.2 years ago by tarek.mohamed270
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gravatar for Gordon Smyth
20 months ago by
Gordon Smyth2.0k
Australia
Gordon Smyth2.0k wrote:

This question was answered on Bioconductor: https://support.bioconductor.org/p/86633/

In summary, Rsubread is a general purpose aligner and is fine for DNA as well as RNA. For DNA, use the Rsubread align() function with `type="dna".

More details about Rsubread are in: https://doi.org/10.1093/nar/gkz114 The article focuses on RNA-seq but DNA-seq is mentioned as well.

We compared Subread with BWA in the original Subread publication: https://doi.org/10.1093/nar/gkt214

ADD COMMENTlink modified 20 months ago • written 20 months ago by Gordon Smyth2.0k
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