Winnowmap for read overlapping

[shelkmike]

Is it possible to use Winnowmap to find overlaps between long reads, equivalent to "ava-ont" and "ava-pb" options of Minimap2? If not, do you plan to add this feature in the future?

[cjain7]

The weighted minimiser idea can be extended for read overlapping as well, but we have never tested.

It should be easy to add back these options in options.c; but testing would need considerable effort. Are you having some example cases where minimap2's masking of repetitive k-mers is leading to undesirable output?

[shelkmike]

I'm assembling a highly repetitive eukaryotic genome by Miniasm. The first step of Miniasm is a search of overlaps between reads, performed by Minimap. I suppose that using Winnowmap may be better, taking into account that many reads originate from repeats.