phase a non-model genome

Question

[devon.orourke]

Hi, I've recently assembled a few non-model organism genomes using a combination of Nanopore and Illumina reads. I was wondering if there are any tools that can phase genomes using the reads alone, without a genetic map. Programs like SHAPEIT require such a file, but for the organisms I work with those don't exist. Perhaps there is a third sequencing technology out there that produces reads that are amenable to phasing (Phase, 10x?). Thanks for any advice you can offer

[devon.orourke]

Wouter, remind me to buy you several adult beverages next time we're at a Nanopore meeting. I owe you - thanks!

[WouterDeCoster]

You're most welcome :-)

(I have moved this reaction you posted. It's not optimal now, but it's the best I can do. You should have used "Add comment" under my answer - and not posted this as a separate answer..)

Answer 1

[WouterDeCoster]

Hi Devon,

Welcome to biostars.
I believe WhatsHap is what you are looking for.

Cheers,
Wouter