Closed yeban closed 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.
What is the
-G
option ofcontigs
command used for? Does it impact assembly quality?