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.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.46.2.
.TH BARRNAP "1" "November 2014" "barrnap 0.4.2" "User Commands"
.SH NAME
barrnap \- rapid ribosomal RNA prediction
.SH SYNOPSIS
barrnap [options] <chromosomes.fasta>
.SH DESCRIPTION
Barrnap predicts the location of ribosomal RNA genes in genomes. It supports
bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and
eukaryotes (5S,5.8S,28S,18S).
.SH OPTIONS
.TP
\fB\-\-help\fR
This help
.TP
\fB\-\-version\fR
Print version and exit
.TP
\fB\-\-citation\fR
Print citation for referencing barrnap
.TP
\fB\-\-kingdom\fR [X]
Kingdom: mito bac arc euk (default 'bac')
.TP
\fB\-\-quiet\fR
No screen output (default OFF)
.TP
\fB\-\-threads\fR [N]
Number of threads/cores/CPUs to use (default '8')
.HP
\fB\-\-lencutoff\fR [n.n] Proportional length threshold to label as partial (default '0.8')
.TP
\fB\-\-reject\fR [n.n]
Proportional length threshold to reject prediction (default '0.5')
.TP
\fB\-\-evalue\fR [n.n]
Similarity e\-value cut\-off (default '1e\-09')
.TP
\fB\-\-incseq\fR
Include FASTA input sequences in GFF3 output (default OFF)