search

Nextomics / NextPolish2

Repeat-aware polishing genomes assembled using HiFi long reads
Other
63 stars 3 forks source link

two phased haplotypes questions #19

Closed Lin-Yuying closed 4 months ago

Lin-Yuying commented 4 months ago

Hi Jiang,

Thank you so much for developing this fantastic tool.

In your example, you used an asm.fa. However, with hifiasm, it yields two phased haplotypes. In this scenario, what would be the recommended approach to rectify switch errors in both haplotypes? Should I run the NextPolish2 pipeline separately for each haplotype?

Thanks in advances!

Best, Lin

moold commented 4 months ago

If your genome is assembled via trio binning. You can discard reads that have different haplotype with the reference before the mapping procedure. If not, just use all reads to do mapping and the default NextPolish2 parameters, It will maintain the same haplotype as ref.