reapr-score1
Calculate scores and assembly errors
Usage
reapr score
[options]
<assembly.fa.gaps.gz>
<in.bam>
<statsprefix>
<FCDcutoff>
<outprefix>
Options
-
-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]
Releases
5 releases since Debian 9 (Stretch); the text changed 4 times.