[Bioc-devel] Question about external algorithms to Bioconductor package

Dario Strbenac dstr7320 at uni.sydney.edu.au
Sun Nov 26 05:00:08 CET 2017

Good day,

> I have DNA data. Is there any other solution rather than Rsubread which is extremely slow?

How much of it do you have? If it's a large size, such as whole genome sequencing, then it would take longer than an RNA-seq experiment regardless of the algorithm you use. I have used Rsubread in the past and I think it performs as well as the other popular alignment programs.

> I am making an algorithm where one of its steps should be to map the DNA reads to the reference genome.

Although it's possible to do short read mapping with packages like Rbowtie, I don't think this preprocessing stage should happen in R which is a statistical programming language. Modularity is good.

Dario Strbenac
University of Sydney
Camperdown NSW 2050

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