skewed binning

[chughes-g]

Hi, I am trying to trio bin my assembly but keep getting binning that favors one parent over the other.

-- Found      48103 reads and   1034301264 bases for haplotype Maternal.
-- Found    4142799 reads and  42575760622 bases for haplotype Paternal.
-- Found     102682 reads and    313446387 bases assigned to no haplotype.
-- Ignored  2201019 reads and   2013520708 bases because they were short.
--
-- Fewer than 5 % of bases in unassigned reads; don't use them in assemblies.

canu -haplotype
-p
-d
genomeSize=1g
useGrid=0
minReadLength=2000
-haplotypeMaternal
-haplotypePaternal
-nanopore-raw \

[skoren]

I'd guess it's picking a bad threshold for coverage for one (or both) of the haplotypes. This usually would happen with low coverage of the parent genomes or if the parents share almost all their k-mers. The haplotype.log file should indicate what threshold it is using. You could then manually correct the threshold (see issues #2345 and #2349)