Parameters for Illumina 2*500bp PE reads

[ksahlin]

Hi @lh3,

I'm benchmarking my aligner against minimap2 and got a reviewer comment about evaluating performance with (eventual) future Illumina chemistry X reads. I am therefore including longer simulated Illumina 2*500bp PE reads. I have so far run my experiments with -x sr. Perhaps the runtime/accuracy tradeoff could be better in minimap2 with different parameters on, e.g., k and w while still being in short-read PE alignment mode.

Any suggestions?