reapr−score − calculate scores and assembly errors
reapr score [options] <assembly.fa.gaps.gz> <in.bam> <statsprefix> <FCDcutoff> <outprefix>
−f <int>
Minimum inner fragment coverage [1]
−g <int>
Max gap length to call over [0.5 * outer_mean_insert_size]
−l <int>
Length of window [100]
−p <int>
Use perfect mapping reads score with given min coverage. Incompatible with −P.
−P <int>
Same as −p, but force the score to be zero at any position with at least the given coverage of perfect mapping reads and which has an OK insert plot, , i.e. perfect mapping reads + insert distribution override all other tests when calculating the score. Incompatible with −p.
−q <float>
Max bad read ratio [0.33]
−r <int>
Min read coverage [max(1, mean_read_cov − 4 * read_cov_stddev)]
−R <int>
Repeat calling cutoff. −R N means call a repeat if fragment coverage is >= N times (expected coverage). Use −R 0 to not call repeats [2]
−s <int>
Min score to report in errors file [0.4]
−u <int>
FCD error window length for error calling [insert_size / 2]
−w <float>
Min percentage of bases in window needed to call as bad [0.8]