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.

[diego-rt]

Hi @cjain7 @lh3

We do have a situation discussed in an issue here where minimap2's masking of high frequency minimisers prevents us from attempting to correct ONT reads at satellites and very abundant repeats.

It would be super useful if we could use winnowmap to generate AvA alignments of ONT reads for correction. I would have some test datasets and I'm happy to carry out some testing.