Input sequences options

-n/--max-ambiguity

Maximum proportion of Ns allowed to attempt analysis. Default: 0.5 (i.e. 50% N content)

-l/--min-length

Minimum query length allowed to attempt analysis. Default: 20000

-ts/--trim-start

Genome position to trim and pad to start from when aligning input sequences. Default: 265

-te/--trim-end

Genome position to trim and pad to at at when aligning input sequences. Default: 29674