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

[Martin Morgan]

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

http://bioconductor.org/packages/release/bioc/html/Rbowtie.html
http://bioconductor.org/packages/release/bioc/html/Rbowtie2.html

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.

Martin


> 
> Thanks
> 


This email message may contain legally privileged and/or...{{dropped:2}}