Clarification in documentation: Polishing phased assemblies about vgp-assembly HOT 4 CLOSED

Hello Dustin,

thanks for reaching out. Even if you have parental data, these are only useful for contigging to initially separate the haplotypes or for evaluation purposes, they should NOT be used for any of the polishing. Note that one of the two parental haplotypes for each parent is NOT inherited, so you'd end with a hybrid of 4 haplotypes in total.

The way this works in VGP is that you combine the two haplotypes, map all your F1 reads simultaneously on both and call variants. This reduces the chances of introducing haplotype switches. We also suggest to check out Merfin, which we recently introduced to improve the quality of the polishing process https://github.com/arangrhie/merfin

from vgp-assembly.

Thank you for the quick reply and saving me a world of future headache. One last question I have is about combining the haplotypes. Do you simply mean making sure the scaffolds have unique identifiers and catting them or is there a more formal type of combining? I think it’s just catting but I figured better safe than sorry.

I’ll definitely check out Merfin! Thank you for the suggestion.

from vgp-assembly.

Hello Dustin, you are right just append a suffix so that your variants will be uniquely assigned to one scaffold per haplotype and then cat them into a single fasta. Good luck!

from vgp-assembly.

Thanks so much! I really appreciate it.

from vgp-assembly.