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Alternative to PASApipeline

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 :)

transcriptomics annotation
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updated by colindaven colindaven • written by lagartija lagartija

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

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written by colindaven colindaven

1 answer

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)

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written by lieven.sterck lieven.sterck

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