We've released version 0.2 last week, which now includes full run-time optimization and a number of small bug-fixes. The previous default to use LoFreq-NQ (quality agnostic EM-based modelling of substitution-type specific error-rates) as pre-filter to LoFreq-Q is now disabled, as LoFreq-Q is now fast enough even in ultra-high coverage regions (>>10k) and produces the same results with and without the filter.