Potential graphaligner/resolution instability

[skoren]

I have two runs of HG002 with slightly different resolutions in the same genomic region with the same input data. The hifi graphs look similar, the new run:

vs the old:

The nodes in question are utig1-43293, utig1-59495 in the new graph and utig1-43264, utig1-59466 in the old graph. In the old graph, both haplotypes are resolved and phased. However, in the new run, the paternal haplotype is broken and has no valid path:

The assemblies are in globus under hg002/asm (original) and hg002/asm_fromscratch (new).

[skoren]

We have a another couple of examples from HG002 where adding ONT data makes some parts of the assembly break. These are on the T2T globus under HG002-Duplex/duplex_50x/asm_3cellONT and asm. Here, chr19 maternal (mat-0000003 in asm_3cellONT) is complete with two telomeres and gapless but adding more ont coverage (mat-0000009 in asm) makes it lose the telomere on one side. Another example from the same assembly, chr7 paternal (pat-0001315 in asm_3cellONT and pat-0001411 in asm) adds a gap with increased coverage around node utig1-28406

[skoren]

And another example under globus for HG002 (asm_newcorrection_repeatbranch vs asm_newcorrection_repeatbranch_rerun) where the region around node utig1-60013 is not resolved in the rerun. The graphs look identical (with same node lengths/counts/edges) and alignments in this region of the ONT reads (alns-ont-mapqfilter.gaf) are the same but in one case, this node has 3 paths using it whereas in the rerun there are 5, leading to an unresolved tangle in the final graph.

[skoren]

I've added some examples of resolutions not in the v2.0 release that were resolved in at least one previous run (from 1.3 to 1.4.1 to v2.0 before correction changes) in hg002/asm_verkko_v2_tip. There's a folder for each chr with a brief description of what assembly/relevant reads for previous resolution. @maickrau if you could take a look at this. The previous example from chr1 is also still present in the v2.0 assembly (comment from Jan 3).