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mcveanlab / mccortex

De novo genome assembly and multisample variant calling
https://github.com/mcveanlab/mccortex/wiki
MIT License
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Use of -G option of contigs command. #46

Closed yeban closed 7 years ago

yeban commented 7 years ago

What is the -G option of contigs command used for? Does it impact assembly quality?

noporpoise commented 7 years ago

Genome size, along with mean read size (stored in the .ctx graph file) are used to calculate contig confidence. Genome size can be guessed from number of kmers in the graph if most of your genome has copy number 1 (e.g. humans).

If you are not using -C, --confid-cumul <C> or -T, --confid-step <T> then it is not used. I'm not sure that these are required as McCortex assembly is quite conservative.

There is a bit of documentation here: https://github.com/mcveanlab/mccortex/wiki/Contig-Assembly

I'll update it now.