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 stage as it is now largely superseded by HISAT2 which provides the 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. 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 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