2017-12-16 10:18 GMT+02:00 Afif Elghraoui <a...@debian.org>: > Hi, all, > > Given the statement from the website [1] > > > Please note that TopHat has entered a low maintenance, low support > > stage as it is now largely superseded by HISAT2 which provides the > > same core functionality (i.e. spliced alignment of RNA-Seq reads), > > in a more accurate and much more efficient way >
This statement is about TopHat 2, which is what is in the Debian package tophat > and a statement from one of its co-authors [2] > > > Please stop using Tophat. Cole and I developed the > > method in *2008*. It was greatly improved in TopHat2 then HISAT > > & HISAT2. There is no reason to use it anymore. I have been > > saying this for years yet it has more citations this year than last > This more strongly worded statement is about TopHat 1, which is not in Debian. We should retain TopHat2, perhaps with a note about HISAT2. > > I think we'd be doing users a favor by removing it from the archive. If > in the future anyone wants to replicate old results based on tophat, > they could build a container off of snapshot.debian.org. > > Are there any objections? > > regards > Afif > > 1. https://ccb.jhu.edu/software/tophat/index.shtml > 2. https://twitter.com/lpachter/status/937055346987712512 > > -- > Afif Elghraoui | عفيف الغراوي > http://afif.ghraoui.name > > -- Michael R. Crusoe Co-founder & Lead, Common Workflow Language project <http://www.commonwl.org/> Direktorius, VšĮ "Darbo eigos", Vilnius, Lithuania https://orcid.org/0000-0002-2961-9670 <https://impactstory.org/u/0000-0002-2961-9670> m...@commonwl.org +1 480 627 9108
