.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH FSA_CTG_BRIDGE "1" "July 2020" "Bridge contigs" "User Commands"
.SH NAME
fsa_ctg_bridge \- Bridge contigs
.SH SYNOPSIS
.B fsa_ctg_bridge
[\fI\,options\/\fR] \fI\,rawreads contigs read2ctg bridged_contigs\/\fR
.SH DESCRIPTION
Command line tool to bridge contigs.


It takes the following parameters:

.IP
rawreads
.IP
	rawread file
.IP
contigs
.IP
	The contig file
.IP
read2ctg
.IP
	The file containing overlaps between rawread and contigs
.IP
bridged_contigs
.IP
	The output file
.SH OPTIONS
.HP
\fB\-\-ctg2ctg_file\fR=\fI\,STRING\/\fR
.IP
filename containing overlaps between contigs
default: ""
.HP
\fB\-\-read_min_length\fR=\fI\,INT\/\fR
.IP
minimum rawread length
default: 10000
.HP
\fB\-\-ctg_min_length\fR=\fI\,INT\/\fR
.IP
minimum contig length
default: 500
.HP
\fB\-\-read2ctg_min_identity\fR=\fI\,DOUBLE\/\fR
.IP
minimum identity of overlaps between rawreads and contigs
default: 80
.HP
\fB\-\-ctg2ctg_min_identity\fR=\fI\,DOUBLE\/\fR
.IP
minimum identity of overlaps between contigs
default: 95
.HP
\fB\-\-read2ctg_max_overhang\fR=\fI\,INT\/\fR
.IP
maximum overhang of overlaps between rawreads and contigs
default: 500
.HP
\fB\-\-ctg2ctg_max_overhang\fR=\fI\,INT\/\fR
.IP
maximum overhang of overlaps between contigs
default: 100
.HP
\fB\-\-read2ctg_min_aligned_length\fR=\fI\,INT\/\fR
.IP
minimum aligned length of overlaps between rawreads and contigs
default: 5000
.HP
\fB\-\-ctg2ctg_min_aligned_length\fR=\fI\,INT\/\fR
.IP
minimum aligned length of overlaps between contigs
default: 2000
.HP
\fB\-\-read2ctg_min_coverage\fR=\fI\,INT\/\fR
.IP
minimum coverage of links between rawreads and contigs
default: 4
.HP
\fB\-\-min_contig_length\fR=\fI\,INT\/\fR
.IP
minimum length of bridged contig
default: 500
.HP
\fB\-\-output_directory\fR=\fI\,STRING\/\fR
.IP
directory for output files
default: "."
.HP
\fB\-\-select_branch=\fR"no|best"
.IP
selecting method when encountering branches in the graph, "no" = do not select any branch, "best" = select the most probable branch
default: "no"
.HP
\fB\-\-dump\fR
.IP
for testing, dump intermediate files
.HP
\fB\-\-thread_size\fR=\fI\,INT\/\fR
.IP
number of threads
default: 4
.PP
Usage: fsa_ctg_bridge [options] rawreads contigs read2ctg bridged_contigs
.IP
rawreads
.IP
rawread file
.IP
contigs
.IP
contig file
.IP
read2ctg
.IP
file containing overlaps between rawread and contigs
.IP
bridged_contigs
.IP
output file
.HP
\fB\-\-ctg2ctg_file\fR=\fI\,STRING\/\fR
.IP
filename containing overlaps between contigs
default: ""
.HP
\fB\-\-read_min_length\fR=\fI\,INT\/\fR
.IP
minimum rawread length
default: 10000
.HP
\fB\-\-ctg_min_length\fR=\fI\,INT\/\fR
.IP
minimum contig length
default: 500
.HP
\fB\-\-read2ctg_min_identity\fR=\fI\,DOUBLE\/\fR
.IP
minimum identity of overlaps between rawreads and contigs
default: 80
.HP
\fB\-\-ctg2ctg_min_identity\fR=\fI\,DOUBLE\/\fR
.IP
minimum identity of overlaps between contigs
default: 95
.HP
\fB\-\-read2ctg_max_overhang\fR=\fI\,INT\/\fR
.IP
maximum overhang of overlaps between rawreads and contigs
default: 500
.HP
\fB\-\-ctg2ctg_max_overhang\fR=\fI\,INT\/\fR
.IP
maximum overhang of overlaps between contigs
default: 100
.HP
\fB\-\-read2ctg_min_aligned_length\fR=\fI\,INT\/\fR
.IP
minimum aligned length of overlaps between rawreads and contigs
default: 5000
.HP
\fB\-\-ctg2ctg_min_aligned_length\fR=\fI\,INT\/\fR
.IP
minimum aligned length of overlaps between contigs
default: 2000
.HP
\fB\-\-read2ctg_min_coverage\fR=\fI\,INT\/\fR
.IP
minimum coverage of links between rawreads and contigs
default: 4
.HP
\fB\-\-min_contig_length\fR=\fI\,INT\/\fR
.IP
minimum length of bridged contig
default: 500
.HP
\fB\-\-output_directory\fR=\fI\,STRING\/\fR
.IP
directory for output files
default: "."
.HP
\fB\-\-select_branch=\fR"no|best"
.IP
selecting method when encountering branches in the graph, "no" = do not select any branch, "best" = select the most probable branch
default: "no"
.HP
\fB\-\-dump\fR
.IP
for testing, dump intermediate files
.HP
\fB\-\-thread_size\fR=\fI\,INT\/\fR
.IP
number of threads
default: 4