the choice of --peak

[zhoudreames]

I have two fully-phased haploid assembly of a diploid specices ,but I only want to polishing one of the two fully-phased haploid genome,How should I choose the parameter “--peak” ，is haploid peak value （43.3）or double of haploid_peak value（86.6）?

[arangrhie]

Hi @zhoudreames,

I'd say provide both haplotype assemblies and provide 43.3. If you only like to polish one haplotype, you could either provide vcf from one haplotype, or drop the filtered vcf from the other haplotype afterwards.

Merfin works best if the assembly matches the kmer spectrum as much as possible. Leaving one haplotype assembly out could cause potential haplotype switching.

Arang

[zhoudreames]

thanks~