Best way to quantify / check the changes unzip does to the assembly

PacificBiosciences / FALCON_unzip

Making diploid assembly becomes common practice for genomic study

BSD 3-Clause Clear License

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Best way to quantify / check the changes unzip does to the assembly #69

Closed roblehmann closed 7 years ago

roblehmann commented 7 years ago

Hey,

as the title says, what is the best way to check the result of the unzipping?

cheers

pb-cdunn commented 7 years ago

Pre-polishing? If you have a reference, I like to run blasr -m1 on the primary and secondary haplotigs. I first run with the example in FALCON-examples/run/greg200k-sv2, installed via FALCON-integrate.

Without a reference, you can compare the primary and secondary haplotigs to each other, which can be interesting.