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cerebis / bin3C

Extract metagenome-assembled genomes (MAGs) from metagenomic data using Hi-C.
GNU Affero General Public License v3.0
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What is the `--tip-size` used for? #38

Open ruoyu1123 opened 2 years ago

ruoyu1123 commented 2 years ago

In contact_map, there is a param named tip-size I cant understand. its value is initialized none and is not input value. But in count_sites, it is used to partition the seq. So could you tell me the means of param ?

cerebis commented 2 years ago

Hi @ruoyu1123 , sorry for taking so long to reply!

--tip-size pertains to a downstream operation that was removed from bin3C and should probably be removed from the UI at this point.

It was used to construct particular type of contact map that was then used to scaffold (order and orientate) contigs. The approach was to convert Hi-C contacts into a traveling salesman problem. I had some success with this idea, but it was not consistent enough to be released in general. The scaffolding operation was moved to a separate program (repo) called scaffold3C, but this tool has never been published or sufficiently validated, sitting idle for a few years now.