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mapleforest / HaploMerger2

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scaffolding before phasing #22

Open baoxingsong opened 5 years ago

baoxingsong commented 5 years ago

The HM2 pipeline phasing firstly and run scaffolding software on the reference haplotype. If you have two contigs of different phases, the scaffolding might join these two contigs together and introduces errors.

So why not run scaffolding software firstly and run the phasing scripts after scaffolding?

mapleforest commented 5 years ago

I am not sure what you mean. With a reference haploid assembly obtained by HM2, you indeed could ran third-party remapping and phasing tools to reconstruct the phased assembly.

But HM2 is not a phasing tool itself.