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tanghaibao / jcvi

Python library to facilitate genome assembly, annotation, and comparative genomics
BSD 2-Clause "Simplified" License
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build pseudochromosome with scaffolds #149

Closed xinshuaiqi closed 5 years ago

xinshuaiqi commented 5 years ago

Hi Haibao, I have a question about using scaffolds to build pseudochromosome using Allmaps.

I already have scaffolds built from contig +Bionano data, here I want to further assembly them to pseudochromosome. And I have a decent genetic map in hand. Shall I use these scaffolds in allmaps with 1) just the genetic map 2)bionano + genetic map. I feel it's redundant to use bionano data again because optical map information has already used in the previous scaffolding process.

I would like to hear your advice on these two options. Thank you very much!

Xinshuai

tanghaibao commented 5 years ago

@xinshuaiqi

My advice is just to just use the genetic map for this one since you already incorporated Bionano data. Additionally, ALLMAPS is indeed most well tested with genetic maps (or multiple genetic maps), while the hybrid (genetic + bionano) mode is possible, it can also have issues at times.

Haibao

xinshuaiqi commented 5 years ago

Thank you very much!