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lemene / PECAT

PECAT, a phased error correct and assembly tool
BSD 2-Clause "Simplified" License
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Polish with short reads illumina #37

Open Karenmagh opened 3 weeks ago

Karenmagh commented 3 weeks ago

Hello, I have a question, is possible polish the primary/alternate and haplo1/haplo2 with illumina reads?

Thanks so much.

lemene commented 3 weeks ago

The primary.fasta and alternate.fasta files can be polished using Illumina data. It's best to concatenate them into a single file and polish them together. This method also applies to haplotype_1.fasta and haplotype_2.fasta.

Karenmagh commented 3 weeks ago

Do you recommend any subsequent method for re-separation? I am considering using Hapo-G (https://github.com/institut-de-genomique/HAPO-G) for polishing.

I would greatly appreciate your response @lemene

lemene commented 3 weeks ago

The contig names are different between primary.fasta and alternate.fasta. After polishing, the contigs can be separated by their names. I have used Pilon but not Hapo-G, so I can't give useful advice on Hapo-G.

Karenmagh commented 3 weeks ago

Thanks so much @lemene , you can close this issue.