Anton Korobeynikov
Anton Korobeynikov
Here is the teaser. While UI shows `BLAST` it's only the UI. The reality is minimap2 under the hood aligning C4 sequences to C4A/C4B graph from https://zenodo.org/record/6617246 The second one...
> out of curiosity, did you use minimap as an API or by calling it as an executable and using IO? Binary is executed and final PAF is parsed. Essentially,...
One need to know though that hit-combining and path-building approaches in Bandage are essentially brute-force :(
Well, not quite :) Overall the problem is similar to that we're having in graph aligning: we have a set of "seed alignments" to the nodes of the graph and...
@ekg Actually it does matter if we need to span a complex repeat :) E.g. in PathRacer we have an option of seeding from paths not nodes and it makes...
@ekg FWIW https://github.com/asl/BandageNG/pull/114 implements alignment to the paths, query paths are automatically built out of the,
@paoloczi Finally this was merged: https://github.com/linuxdeploy/linuxdeploy-plugin-qt/pull/118, so likely the issue will be fully resolved with Bandage 2022.08
@paoloczi Will you please check if https://github.com/asl/BandageNG/releases/tag/v2022.08 works for you now?
@paoloczi Oh, the cmdline interface requires lots of care.... it's broken in many places and not quite complete. But this is a separate issue – #50
> Mesh can reclaim on SPades (over a GB), neat! How I can see it? Is this "Meshed MB HWM" value? > /proc/sys/vm/max_map_count and sets a limit on the number...