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

Question

[tarek.mohamed]

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

Answer 1

[Gordon Smyth]

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