Filters - Low quality overlap filtering
fsa_ol_filter [options] overlaps
filtered_overlaps
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
--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