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vgteam / long-read-giraffe-experiments

Experimental materials for testing the long-read mapping abilities of vg giraffe
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Use optimal Minimap2 parameters #14

Closed adamnovak closed 2 months ago

adamnovak commented 6 months ago

See https://ucsc-gi.slack.com/archives/CJ2EHEH1A/p1715041620584409 and other notes about the current best version and parameters of minimap2

adamnovak commented 6 months ago

We probably need lr:hq from https://github.com/lh3/minimap2/releases/tag/v2.27 and later

adamnovak commented 6 months ago

We now have lr:hqae, but we might actually want to be using lr:hq for nanopore R10 and something else for R9?

Also lr:hqae is "assembly evaluation", so if we are aligning to a different assembly we might want a different mode.