Anyone knows any QC pipeline for PacBio data as well as pipeline for de novo assembly? #consgen #popgen - ThreadSky

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sagitaninta.bsky.social • 23 days ago

Anyone knows any QC pipeline for PacBio data as well as pipeline for de novo assembly?

#consgen #popgen

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It's been a minute since I've done a pacbio assembly, but flye was a great assembler to use (hopefully that's still the case). Regarding QC, fastp has a long-read version.

pvdimens.bsky.social•21 days ago

I realize now that your question might be more specific to pipeline and not individual software. Unfortunately, I'm unfamiliar with the existing pipeline landscape 😔

sagitaninta.bsky.social•21 days ago

No worries, thanks for chiming in! At least I know where to start looking from there 😁

reptilerhett.bsky.social•21 days ago

Hi! PacBio bioinformatics support scientist here specializing on genome assembly.

QC reports are mainly generated on-instrument or in SMRT Link. Whoever you did your sequencing with, should be able to provide you with a QC report. There is no trimming or external QC needed.

reptilerhett.bsky.social•21 days ago

Typically I would recommend hifiasm for assembly. It’s fast and produces the highest quality assemblies.

Hope this helps!

marcopessoa.bsky.social•21 days ago

I'm not aware of any single pipeline for the whole process, but if you have CCS HiFi reads, hifiasm would be my assembler of choice.

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