NAME

       Filters - Low quality overlap filtering

SYNOPSIS

       fsa_ol_filter [options] overlaps filtered_overlaps

DESCRIPTION

       Command line tool to filters out low-quality overlaps prior to assembling.

       This takes the following parameters:

              overlaps

                   The input filename

              filtered_overlaps

                   The resulting ouput filename

OPTIONS

       --min_length=INT

              minimum length of reads

              default: 2500

       --max_length=INT

              maximum length of reads default: 2147483647

       --min_identity=DOUBLE

              minimum identity of overlaps

              default: 90

       --min_aligned_length=INT

              minimum aligned length of overlaps default: 2500

       --max_overhang=INT

              maximum overhang of overlaps, negative number = determined by the program.

              default: 10

       --min_coverage=INT

              minimum base coverage, negative number = determined by the program.  default: -1

       --max_coverage=INT

              maximum base coverage, negative number = determined by the program default: -1

       --max_diff_coverage=INT

              maximum difference of base coverage, negative number = determined by the program default: -1

       --coverage_discard=DOUBLE

              discard ratio of base coverage. If max_coverage or max_diff_coverage is negative, it will be reset
              to (100-coverage_discard)th percentile.  default: 0.01

       --overlap_file_type="|m4|m4a|paf|ovl"

              overlap  file  format.  "" = filename extension, "m4" = M4 format, "paf" = PAF format generated by
              minimap2, "ovl" = OVL format generated by FALCON.  default: ""

       --bestn=INT

              output best n overlaps on 5' or 3' end for each read

              default: 10

       --genome_size=INT

              genome size. It determines the maximum length of reads with coverage together default: 0

       --coverage=INT

              coverage. It determines the maximum length of reads with genome_size together default: 0

       --output_directory=STRING

              directory for output files default: "."

       --thread_size=INT

              number of threads default: 4

       Usage: fsa_ol_filter [options] overlaps filtered_overlaps

              overlaps

              input filename

              filtered_overlaps

              ouput filename

       --min_length=INT

              minimum length of reads

              default: 2500

       --max_length=INT

              maximum length of reads default: 2147483647

       --min_identity=DOUBLE

              minimum identity of overlaps

              default: 90

       --min_aligned_length=INT

              minimum aligned length of overlaps default: 2500

       --max_overhang=INT

              maximum overhang of overlaps, negative number = determined by the program.

              default: 10

       --min_coverage=INT

              minimum base coverage, negative number = determined by the program.  default: -1

       --max_coverage=INT

              maximum base coverage, negative number = determined by the program default: -1

       --max_diff_coverage=INT

              maximum difference of base coverage, negative number = determined by the program default: -1

       --coverage_discard=DOUBLE

              discard ratio of base coverage. If max_coverage or max_diff_coverage is negative, it will be reset
              to (100-coverage_discard)th percentile.  default: 0.01

       --overlap_file_type="|m4|m4a|paf|ovl"

              overlap file format. "" = filename extension, "m4" = M4 format, "paf" = PAF  format  generated  by
              minimap2, "ovl" = OVL format generated by FALCON.  default: ""

       --bestn=INT

              output best n overlaps on 5' or 3' end for each read

              default: 10

       --genome_size=INT

              genome size. It determines the maximum length of reads with coverage together default: 0

       --coverage=INT

              coverage. It determines the maximum length of reads with genome_size together default: 0

       --output_directory=STRING

              directory for output files default: "."

       --thread_size=INT

              number of threads default: 4

Filters out low-quality overlaps for assembling     July 2020                                         FILTERS(1)