Grouping scaffolds into chromosomes

[kkrizanovic]

hello,

I'm trying to assemble a plant genome of roughly 4Gbp with 11 chromosomes. ATM I'm working on haploid assembly.

I've got about 3000 contings using hifiasm, and SALSA produced about 1600 scaffolds.

Is there a way to group those scaffolds into chromosome?

[skoren]

There isn't a way to group contigs beyond the scaffolding done in SALSA. If it didn't group them, then it likely reached the stopping condition where no useful links were left from the HiC data. I wouldn't rely on the raw count of contigs/scaffolds but instead check what fraction of the genome is in the largest scaffolds. It may be that most of the sequences are already scaffolded. You may also need to run purge_dups to remove some remaining haplotype duplications before scaffolding.