reapr-break - make broken assembly via REAPR
reapr break [options] <assembly.fa>
<errors.gff.gz> <outfileprefix>
<errors.gff.gz> is the errors GFF file made when running
score.
-a
Aggressive breaking: break contigs at any FCD or low_frag
error, as opposed to the default of replacing with Ns. Contigs are broken at
the midpoint of each error. Also see option -t. Incompatible with
-b.
-b
Ignore FCD and low fragment coverage errors that do not
contain a gap (the default is to replace these with Ns). Incompatible with
-a.
-e <float>
Minimum FCD error [0]
-l <int>
Minimum sequence length to output [100]
-m <int>
Max sequence length to write to the bin. Sequences longer
than this are written to the main assembly output. This is to stop long
stretches of sequence being lost [999]
-t <int>
When -a is used, use this option to specify how
many bases are trimmed off the end of each new contig around a break.
-t N means that, at an FCD error, a contig is broken at the middle
coordinate of the error, then N bases are trimmed off each new contig end
[0]