Scaffolded by 3D-DNA or HiRise in unphased assembly

[xingjianfeng100]

Dear author The paper "Accurate chromosome-scale haplotype-resolved assembly of human genomes " described there was a step that grouping and ordering contigs into scaffolds with Hi-C data using HiRise/3D between "Assemble HiFi reads into unphased contigs using Peregrine" and "map HiFi reads to scaffolds and call heterozygous SNPs using DeepVariant ". But I noticed that pipeline.sh (https://github.com/shilpagarg/DipAsm/blob/master/pipeline.sh) has skipped this step. Could you tell me if there are something wrong or my errant understanding? Looking forward to your reply.