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Rsubread versus BWA ( Burrows-Wheeler Alignmener) for whole genome alignment

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

rsubread bwa ngs
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updated by Gordon Smyth Gordon Smyth • written by tarek.mohamed tarek.mohamed

1 answer

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

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written by Gordon Smyth Gordon Smyth

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