NAME

       reapr-break - make broken assembly via REAPR

SYNOPSIS

       reapr break [options] <assembly.fa> <errors.gff.gz> <outfileprefix>

DESCRIPTION

       <errors.gff.gz> is the errors GFF file made when running score.

OPTIONS

       -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]

SEE ALSO

       reapr(1)

                                                                                   REAPR-BREAK(1)