Alternative to PASApipeline

Question

[lagartija]

Hi all,

I just wanted to chat about eukaryotic genome annotation using funannotate hence PASA. PASA is hard to configure and I always run into different errors. It is also slow. Yet, when it works, it is very powerful ! Do you know any alternative to PASApipeline that would work as good?

Thanks :)

[colindaven]

I don't think there are any direct alternatives to PASA with its' concept of alignment assemblies.

Answer 1

[lieven.sterck]

I'm not sure if there are any one-to-one replacements for PASA but there are for sure other tools that can do transcript alignment/reconstruction:

• STAR
• trans-ABYSS
• Trinity
• StringTie
• ...

and there are likely others as well. Depending on your goals you might need to do a 2-step approach, eg first assemble reads to transcripts (with tool A) and map those to genome (tool B)