reapr-break1
Make broken assembly via reapr
Usage
reapr break
[options]
<assembly.fa>
<errors.gff.gz>
<outfileprefix>
Overview
<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
-ais used, use this option to specify how many bases are trimmed off the end of each new contig around a break.-tN 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]
Releases
5 releases since Debian 9 (Stretch); the text changed 4 times.