Using HiFi + Hi-C Hifiasm assembly as input

ShunOuchi / GreenHill

De novo chromosome-level scaffolding and phasing tool using Hi-C

GNU General Public License v3.0

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Using HiFi + Hi-C Hifiasm assembly as input #37

Closed foreignsand closed 2 months ago

foreignsand commented 3 months ago

Apologies if this is covered somewhere and I missed it, but I couldn't find information about using a phased HiFi + Hi-C Hifiasm assembly as input for GreenHill. Would it be considered haplotype-aware style input?

Many thanks!

ShunOuchi commented 3 months ago

Briefly, I recommend to run GreenHill using the -cph option with the hap1 + hap2 of hifiasm as input.

greenhill -cph hifiasm.hic.hap1.p_ctg.fa hifiasm.hic.hap2.p_ctg.fa -p HiFi.fq -HIC HIC_1.fq HIC_2.fq

Please see https://github.com/ShunOuchi/GreenHill/issues/15#issuecomment-1647277283 for details.

Thank you