On December 20, 2017 5:17:20 AM EST, Michael Crusoe <[email protected]> wrote: >2017-12-16 10:18 GMT+02:00 Afif Elghraoui <[email protected]>: > >> 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 stage as it is now largely superseded by HISAT2 which provides the 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. >
The summary of the statement is that hisat2 is the only one of those 4 that isn't obsolete, and therefore that it's the only one of those 4 that should be used. >We should retain TopHat2, perhaps with a note about HISAT2. > I think tophat2 (and hisat1 if we have it) should also be removed. We should get upstream involved if you still disagree. regards Afif
