.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.16.
.TH FILTERS "1" "July 2020" "Filters out low-quality overlaps for assembling" "User Commands"
.SH NAME
Filters \- Low quality overlap filtering
.SH SYNOPSIS
.B fsa_ol_filter
[\fI\,options\/\fR] \fI\,overlaps filtered_overlaps\/\fR
.SH DESCRIPTION
Command line tool to filters out low\-quality overlaps prior to assembling.

This takes the following parameters:

.IP
overlaps
.IP
	The input filename
.IP
filtered_overlaps
.IP
	The resulting ouput filename
.SH OPTIONS
.HP
\fB\-\-min_length\fR=\fI\,INT\/\fR
.IP
minimum length of reads
.IP
default: 2500
.HP
\fB\-\-max_length\fR=\fI\,INT\/\fR
.IP
maximum length of reads
default: 2147483647
.HP
\fB\-\-min_identity\fR=\fI\,DOUBLE\/\fR
.IP
minimum identity of overlaps
.IP
default: 90
.HP
\fB\-\-min_aligned_length\fR=\fI\,INT\/\fR
.IP
minimum aligned length of overlaps
default: 2500
.HP
\fB\-\-max_overhang\fR=\fI\,INT\/\fR
.IP
maximum overhang of overlaps, negative number = determined by the program.
.IP
default: 10
.HP
\fB\-\-min_coverage\fR=\fI\,INT\/\fR
.IP
minimum base coverage, negative number = determined by the program.
default: \fB\-1\fR
.HP
\fB\-\-max_coverage\fR=\fI\,INT\/\fR
.IP
maximum base coverage, negative number = determined by the program
default: \fB\-1\fR
.HP
\fB\-\-max_diff_coverage\fR=\fI\,INT\/\fR
.IP
maximum difference of base coverage, negative number = determined by the program
default: \fB\-1\fR
.HP
\fB\-\-coverage_discard\fR=\fI\,DOUBLE\/\fR
.IP
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
.HP
\fB\-\-overlap_file_type=\fR"|m4|m4a|paf|ovl"
.IP
overlap file format. "" = filename extension, "m4" = M4 format, "paf" = PAF format generated by minimap2, "ovl" = OVL format generated by FALCON.
default: ""
.HP
\fB\-\-bestn\fR=\fI\,INT\/\fR
.IP
output best n overlaps on 5' or 3' end for each read
.IP
default: 10
.HP
\fB\-\-genome_size\fR=\fI\,INT\/\fR
.IP
genome size. It determines the maximum length of reads with coverage together
default: 0
.HP
\fB\-\-coverage\fR=\fI\,INT\/\fR
.IP
coverage. It determines the maximum length of reads with genome_size together
default: 0
.HP
\fB\-\-output_directory\fR=\fI\,STRING\/\fR
.IP
directory for output files
default: "."
.HP
\fB\-\-thread_size\fR=\fI\,INT\/\fR
.IP
number of threads
default: 4
.PP
Usage: fsa_ol_filter [options] overlaps filtered_overlaps
.IP
overlaps
.IP
input filename
.IP
filtered_overlaps
.IP
ouput filename
.HP
\fB\-\-min_length\fR=\fI\,INT\/\fR
.IP
minimum length of reads
.IP
default: 2500
.HP
\fB\-\-max_length\fR=\fI\,INT\/\fR
.IP
maximum length of reads
default: 2147483647
.HP
\fB\-\-min_identity\fR=\fI\,DOUBLE\/\fR
.IP
minimum identity of overlaps
.IP
default: 90
.HP
\fB\-\-min_aligned_length\fR=\fI\,INT\/\fR
.IP
minimum aligned length of overlaps
default: 2500
.HP
\fB\-\-max_overhang\fR=\fI\,INT\/\fR
.IP
maximum overhang of overlaps, negative number = determined by the program.
.IP
default: 10
.HP
\fB\-\-min_coverage\fR=\fI\,INT\/\fR
.IP
minimum base coverage, negative number = determined by the program.
default: \fB\-1\fR
.HP
\fB\-\-max_coverage\fR=\fI\,INT\/\fR
.IP
maximum base coverage, negative number = determined by the program
default: \fB\-1\fR
.HP
\fB\-\-max_diff_coverage\fR=\fI\,INT\/\fR
.IP
maximum difference of base coverage, negative number = determined by the program
default: \fB\-1\fR
.HP
\fB\-\-coverage_discard\fR=\fI\,DOUBLE\/\fR
.IP
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
.HP
\fB\-\-overlap_file_type=\fR"|m4|m4a|paf|ovl"
.IP
overlap file format. "" = filename extension, "m4" = M4 format, "paf" = PAF format generated by minimap2, "ovl" = OVL format generated by FALCON.
default: ""
.HP
\fB\-\-bestn\fR=\fI\,INT\/\fR
.IP
output best n overlaps on 5' or 3' end for each read
.IP
default: 10
.HP
\fB\-\-genome_size\fR=\fI\,INT\/\fR
.IP
genome size. It determines the maximum length of reads with coverage together
default: 0
.HP
\fB\-\-coverage\fR=\fI\,INT\/\fR
.IP
coverage. It determines the maximum length of reads with genome_size together
default: 0
.HP
\fB\-\-output_directory\fR=\fI\,STRING\/\fR
.IP
directory for output files
default: "."
.HP
\fB\-\-thread_size\fR=\fI\,INT\/\fR
.IP
number of threads
default: 4