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

Martin Morgan martin.morgan at roswellpark.org
Fri Nov 24 19:11:24 CET 2017

On 11/24/2017 09:57 AM, Ioannis Vardaxis wrote:
> Hi,
> I tried the Rsubread package you suggested and the mapping is running.
> However it takes like forever to end. Even in parallel it needs some days
> to run while bowtie for example needs only a couple of hours in 4 cores.
> Is there any way of speeding up Rsubread? Or else I don¹t see any reason
> using it, and this is a big problem if I cannot use bowtie inside a
> bioconductor package.

I'm not following this thread closely but there are two Bowtie 
implementations in Bioconductor


The fast solution for many problems (mapping to known transcripts) is 
kalisto / salmon, which are not available in Bioconductor -- integrating 
either of these as _libraries_ would be a nice package.


> Thanks

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