fsa_ctg_bridge - Bridge contigs
fsa_ctg_bridge [options] rawreads contigs
read2ctg bridged_contigs
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
--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