Options for long-read diploid assembly

Question

[predeus]

Hello all,

I was wondering about the options for ploidy-aware assemblers for long reads. I know there is FALCON-unzip for Pacbio, and I also have seen a recent preprint. What are other options for highly heterozygous genomes? Thank you in advance!

[WouterDeCoster]

I'm not aware of any other diploid long read assemblers - it's a quite new concept.

Answer 1

[Buffo]

Probably CLC Genomics Workbench and HGAP are the best choices for long leads.

[predeus]

Not just long reads - there's plenty of assemblers for that (and, no offence, but I would not rank the options you mentioned too highly - miniasm-racon is way faster, and Flye and Canu a a lot more user friendly and generate better results). However, I was interested in tools specifically geared towards resolving haplotypes for highly heterozygous organisms.

Answer 2

[harish]

You can created a smashed haplotype from Canu and later use WhatsHAP or similar approaches. But other than that IIRC, Falcon/Unzip is the only method.

Also if you have parental samples, you can check trio-binning approach as well.