Hello,
I will have to align PacBio full-length transcripts against a reference.
I'm gonna use the isoseq3 pipeline in order to map my full-length transcripts against my reference, is it the good workflow?
My other question is : do you have an idea of the necessary time to assemble a 500Mb diploide genome with the smrtlink package? Or should I use another package like canu or hifiasm?
Bests
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written
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pablo
1 answer
This is strongly dependent on your infrastructure. How big is your cluster / or single server ? Why not just try it ? I haven't used isoseq3 but am a big fan of gmap with the GFF3 option for transcript to reference mapping. Evaluation by eye in a web browser is critical.
Generally though, assembly will take a lot longer than mapping. Canu can take weeks for 3 GB haploid genomes with ONT reads.
If you want an answer to your assembly question you'll have to provide many more details.
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