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]