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phase a non-model genome

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

phasing
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written by devon.orourke • devon.orourke

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

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written by devon.orourke • devon.orourke

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..)

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written by WouterDeCoster WouterDeCoster

1 answer

Hi Devon,

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

Cheers,
Wouter

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written by WouterDeCoster WouterDeCoster

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