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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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Split chimeric chromosomes #122

Closed francicco closed 3 years ago

francicco commented 5 years ago

Hi,

AllMaps was very successfully able to super-scaffold my assembly using the synteny map with a reference genome. AllMaps scaffolded my scaffolds into 21 pseudochromosomes + 276 minor scaffolds. The 21 pseudochromosomes are exactly the number of chrs as in the reference; since my species has 31 chrs, that means there are clearly some chrs artificially joined. Is there a way to split those pseudochromosomes?

Thanks F

tanghaibao commented 5 years ago

@francicco

You need to somehow identify where the splits may be. Obviously, if you use a 21-chr reference, it will just end up having a 21-chr assembly.

Do you happen to have a genetic map that has 31 linkage groups?

Haibao

francicco commented 5 years ago

Hi @tanghaibao,

I think there should be available a linkage map for my species, but I not sure I use it I never did. I was also thinking at reapr, would it help?

Thanks F

tanghaibao commented 5 years ago

@francicco

Finding breakpoints based on paired reads (such as using reapr) might work. My worry is that it may end up giving you way too many candidate splits than you want (in your case, 10 splits) due to repeats and inaccuracy in read mapping. It's worth trying though.

Haibao

francicco commented 5 years ago

I'm trying, let's see. F