---
name: "fsa_ol_filter"
section: "1"
platform: "linux"
package: "mecat2"
version: "0.0+git20200428.f54c542+ds-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fsa_ol_filter"
---

# fsa\_ol\_filter(1)

Low quality overlap filtering

## 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