Man page - fsa_ol_filter(1)
Packages contains this manual
Manual
FILTERS
NAMESYNOPSIS
DESCRIPTION
OPTIONS
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