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ababaian / LIONS

LIONS is a bioinformatic analysis pipeline which brings together a few pieces of software and some home-brewed scripts to annotate a paired-end RNAseq library to detect TE-intiated transcripts
GNU General Public License v3.0
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Any plans to switch to HISAT2? #16

Closed Alex-Nesta closed 4 years ago

Alex-Nesta commented 4 years ago

Tophat is pretty slow and old, are you planning to use hisat2 instead in the future?

ababaian commented 4 years ago

There is a rumor of a post-doc in france who is re-writing LIONS for HISAT/stringtie and will greatly simplify the usage and installation. I'll shoot an email and see what the progress is on the update.

ababaian commented 4 years ago

This is somewhere in the pipeline, but it might take a while. I'm not planning on writing a switch, but goodness knows it would be helpful.