Dear all,

has anyone done any benchmarking on speeding up long read alignment algorithms ?

I mainly use minimap2, but its' runtime varies by a factor of 10 across our cluster. I've been trying mm2-fast https://github.com/bwa-mem2/mm2-fast, the partially accelerated version, but without much success so far.

Is for example PAF output faster than SAM ?

Have others worked out how to scale minimap2 for Promethion scale datasets ? I expect LRA https://github.com/ChaissonLab/LRA has a similar runtime from their presented results, and others seem slower still (ngmlr etc).

Thanks
1) Yes, when Minimap2 makes paf files it is faster than when it makes sam files.<br>
2) For a speedup at cost of accuracy you can increase the minimizer length ("-k") and window length ("-w").<br>
3) You can increase "-I". If the reference is larger than 4 Gbp, this will accelerate Minimap2 at cost of increased RAM consumption.<br>
<br>
Also, see https://github.com/lh3/minimap2/issues/322