Man page - reapr-break(1)

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Package: reapr
apt-get install reapr

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reapr

Manual

REAPR-BREAK

NAME
SYNOPSIS
DESCRIPTION
OPTIONS
SEE ALSO

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]