reapr break [options] <assembly.fa> <errors.gff.gz> <outfileprefix>
<errors.gff.gz> is the errors GFF file made when running score.
- 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.
- Ignore FCD and low fragment coverage errors that do not contain a gap (the default is to replace these with Ns). Incompatible with -a.
- Minimum FCD error 
- Minimum sequence length to output 
- 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 
- 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