FORUMFavorite splice aware alignment program for RNA-Seq?
mattdoug asked 4 years ago

TopHat, STAR, HISAT, something else? What program(s) have you used, and did you pick them for a particular reason?

3 Answers
zhibin Staff answered 4 years ago

I used them all but my favorite becomes hisat recently. It is fast with low memory requirement. I think people use star because of the speed but it uses too much memory. The alignment speed for hisat is compatible with star.

jflucier Staff answered 4 years ago

You could also look at this post that is related to your question:

jrosner Staff answered 4 years ago

You can also have a look at this Nature paper (2013) that takes a deep dive into evaluating various splice alignment tools and this PMC article (2014) that looks at differential splice analysis tools.
perhaps slightly outdated, but likely still relevant.