Preset (-x) adap: adaptive, for short or mixed-length readssr: short readslr: long reads (not paired) Threads (-t) Batch size, million bases (-K)

Threads need a browser that allows shared memory; more than the machine has only slows the run. A small batch makes the plots advance steadily, while minibwa's own 100 delivers reads in rare bursts.

Min seed length (-k) Max seed occurrences (-c)

Shorter seeds find more alignments in divergent reads but cost time; a lower occurrence limit speeds up repetitive genomes at the price of missing repeats.

Match score (-A) Mismatch penalty (-B) Gap open penalty (-O, first) Gap open penalty (-O, second) Gap extension penalty (-E, first) Gap extension penalty (-E, second)

A gap of length k costs the lesser of open + k × extend over the two pairs.

Map each read alone: skip pairing and mate rescue (-P)

These apply to the next run; the index is not affected. Only options that differ from minibwa's defaults are passed on its command line, which the log shows.