phasegenomics / FALCON-Phase

FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds
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Workflow #83

Open Yutang-ETH opened 2 years ago

Yutang-ETH commented 2 years ago

Hi,

I read from the falcon-phase paper, the suggested workflow is following:

  1. partially phased assembly
  2. falcon-phase on primary contigs and haplotigs
  3. hi-c scaffolding
  4. 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