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