use falcon-unzip for tetraploid

PacificBiosciences / FALCON_unzip

Making diploid assembly becomes common practice for genomic study

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use falcon-unzip for tetraploid #33

Open tangerzhang opened 8 years ago

tangerzhang commented 8 years ago

Hi, Is it possible to use falcon-unzip for tetraploid or hexaploid genome assembly and phasing? Jason gave me a short answer: you cat get haplotype-fused contigs but not haplotype seperated halpotigs. May I have more information?

pb-jchin commented 8 years ago

please see https://speakerdeck.com/jchin/pagxxiv-2016-bioinformatics-workshop during FALCON, it does not using any SNP information to layout contigs. For polyploid genome, as long as there is difference between different haplotype remains small, they will create a single "bundle" in the assembly graph and we can layout the contigs regardless the ploidy, but the next step uses the assumption there are only two haplotypes.