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nadegeguiglielmoni / GraphUnzip

Unzip assembly graphs with Hi-C data and/or long reads.
GNU General Public License v3.0
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Plans for Omni-C data? #18

Closed talioto closed 1 year ago

talioto commented 2 years ago

Hi Nadège and Jean-François,

Are there any plans to support Omni-C? As it stands, GraphUnzip expects a fragment list, which of course would be ridiculous for Omni-C. I'd like to try GraphUnzip on Flye GFA output, but we only use Omni-C in-house. Of course I could just use the ONT reads again, but I'd like to try the Hi-C interaction matrix option.

-Tyler

nadegeguiglielmoni commented 2 years ago

Hello,

You can already use Omni-C data. When processing the reads with hicstuff, use a value for -e, something around 100-1000 bp. Then your fragments will just be arbitrary fragments of this size.