David Eccles 🌻🇵🇸7x🩹🛡️ @gringene.org · May 29 1 / 3
These need a bit more workshopping; the longest mahmoudi sequence is missing bits, with 10k banding and lots of N patches; the chili sequence is similar, with more breaks. It's been a while since I've looked at a chromosome larger than a gigabase with REPAVER; seems like it's still working okay.
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"chromosome assignment was performed using sourmash k-mer containment rather than whole-genome alignment tools, which failed due to the 32-bit integer limit of minimap2 (2,147,483,647 bp) on 10+ Gbp polyploid genomes." I learnt that lesson *years* ago with REPAVER; it uses 64-bit location indexing.