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