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