Documentation for use of genetic map information to phase haplotypes in polyploids

[marcopessoa]

The supplementary file of Cheng et al. 2024 mentions the option "-5" for using genetic map information to phase polyploid haplotypes. However, documentation about this option is missing in hifiasm.

The Readme at https://github.com/baozg/Potato_C88 and their paper (https://doi.org/10.1038/s41588-022-01015-0) describe how they did that for the autotetraploid potato genome, but I wonder if detailed documentation for other use cases will be available. For instance, should one follow the same methods to obtain a genetic map as in Sun et al. 2022 (namely sequencing a mapping population, estimating dosage for haplotigs, and then building the map), or would a phased genetic map obtained with GBS also be helpful?

[chhylp123]

I will have a try to update hifiasm document in coming weeks. The current version of document is 0.16.1, which is quite old in comparison with its own version. This month is quite busy...