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ccgproject / ccgp_assembly

CCGP Repository for the genome assembly working group.
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Question About Use of BlobToolKit #1

Closed foreignsand closed 2 weeks ago

foreignsand commented 7 months ago

In the flowchart depicting the pipeline used by CCGP for genome assembly, there is a line connecting the 'Contamination Screening: BlobToolKit' box to the 'ARIMA Mapping Pipeline' box. This suggests that HiC reads are mapped to contigs produced by HiFiasm after they have been decontaminated using BlobToolKit. Is this correct?

I find the BlobToolKit docs to be a bit opaque and am hoping I can avoid puzzling out the pipeline for a little while longer.

Cheers, Emily

merlyescalona commented 5 months ago

Hi, yes, that's correct. I'll update the Blobtools section as soon as I can describing how I have it working. It is the simplest configuration I could set up.

In any case, I'd recommend to check this: https://pipelines.tol.sanger.ac.uk/blobtoolkit .

foreignsand commented 5 months ago

Great! I've looked at the blobtoolkit pipeline and it's a bit esoteric. Any guidelines you can provide would be much appreciated.

Thanks so much!

Cheers, Emily