Workflow #83
Description
Hi,
I read from the falcon-phase paper, the suggested workflow is following:
- partially phased assembly
- falcon-phase on primary contigs and haplotigs
- hi-c scaffolding
- falcon-phase again on scaffolds
My question is could we skip step 2? I first used hi-c data to scaffold the primary assembly and then applied falcon-phase to phase scaffolds and haplotigs. The reason why I would like to skip step 2 is because there're many mis-joins in the primary contigs, by doing Hi-C scaffolding, I could break some mis-joins.
Could you please show me your ideas? Thank you very much.
Best wishes,
Yutang