Given the statement from the website 
> 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 stage as it is now largely superseded by HISAT2 which provides the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
and a statement from one of its co-authors 
> 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
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?
Afif Elghraoui | عفيف الغراوي