Re: removing tophat from Debian
On December 20, 2017 5:17:20 AM EST, Michael Crusoe <michael.crusoe@gmail.com> wrote:
>2017-12-16 10:18 GMT+02:00 Afif Elghraoui <afif@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 stage as it is now largely superseded by HISAT2 which provides the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.
>
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
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