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BGI-Qingdao / TGS-GapCloser

A gap-closing software tool that uses long reads to enhance genome assembly.
GNU General Public License v3.0
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Use pre-assembled contigs for gap filling #85

Open chenzixi07 opened 2 months ago

chenzixi07 commented 2 months ago

Dear developer, 1) If I use hifiasm+hifi data+ont data as the main assembly. I wonder if I cound use the assembled contigs by other tools like nextdenovo, verkko, hicanu as the input file for "--reads"? If so, what parameter should I use for the "--tgstype" option? Since some tools use both hifi data+ont data to assemble. Can I concat all the contigs by nextdenovo, verkko, hicanu, and run only once?

2) For hifi reads, ont reads, and assembled contigs, which data should be used first. second, and third? Or I could use them in random order?

Thanks, Zixi

DayTimeMouse commented 1 month ago

Hi chenzixi07,

Do you have any ideas for these issue now? I am also interested in that.