Whole Genome Haplotyping
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4.6 years ago

Hello,

I'm currently looking for recommendations on a method for haplotyping. The input is a .sam file with reads mapped to a (known) reference. The reads come from a species with 2 haplotypes (human), rather than reconstructing the genome I want to reconstruct its both haplotypes.

The reads are long (~10,000 bp) with high error rate and lots of indels (3-15%, nucleotides are errors, a majority are indels).

I've found one in https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073643/ but do not seem to be publicly available for download. Primarily I have problems to find what methods right now are considered the best, as well as being easy to install and use.

Assembly sequencing genome Haplotyping • 958 views
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Why don't you explicitly write which technology was used? We can guess on nanopore data, but there is no need to be obscure about it.

Have a look at WhatsHap, I haven't used it though.

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Sorry, Pacific Biosciences Real-time Sequencer.

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So Falcon Unzip maybe?

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Thank you, will try that one.

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Seems like the program is currently under development and very much not trivial to use. Do you know about something for the slightly less tech-savy? (Like Bwa-Mem and samtools, those I can handle)

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Actually I want to do the same (in other species), I had work with illumina and PacBio reads before and I think that the best way to do that is sequencing chromosomes separately, at least you have an overall RDC higher than 500x. You can see disPades assembler, it is a good aproximation https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4449708/