---
name: "filtlong"
section: "1"
platform: "linux"
package: "filtlong"
version: "0.2.1-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/filtlong"
---

# filtlong(1)

quality filtering tool for Nanopore and PacBio reads

## NAME

filtlong - quality filtering tool for Nanopore and PacBio reads

## SYNOPSIS

**filtlong** {OPTIONS} \[input\_reads\]

## OPTIONS

### positional arguments:

- input\_reads

  input long reads to be filtered

### optional arguments:

-

  output thresholds:

- **-t\[int\]**, **--target\_bases** \[int\]

  keep only the best reads up to this many total bases

- **-p\[float\]**, **--keep\_percent** \[float\]

  keep only this percentage of the best reads (measured by bases)

- **--min\_length** \[int\]

  minimum length threshold

- **--min\_mean\_q** \[float\]

  minimum mean quality threshold

- **--min\_window\_q** \[float\]

  minimum window quality threshold

-

  external references (if provided, read quality will be determined using these instead of from the Phred scores):

- **-a\[file\]**, **--assembly** \[file\]

  reference assembly in FASTA format

- **-1\[file\]**, **--illumina\_1** \[file\]

  reference Illumina reads in FASTQ format

- **-2\[file\]**, **--illumina\_2** \[file\]

  reference Illumina reads in FASTQ format

-

  score weights (control the relative contribution of each score to the final read score):

- **--length\_weight** \[float\]

  weight given to the length score (default: 1)

- **--mean\_q\_weight** \[float\]

  weight given to the mean quality score (default: 1)

- **--window\_q\_weight** \[float\]

  weight given to the window quality score (default: 1)

-

  read manipulation:

- **--trim**

  trim non-k-mer-matching bases from start/end of reads

- **--split** \[split\]

  split reads at this many (or more) consecutive non-k-mer-matching bases

-

  other:

- **--window\_size** \[int\]

  size of sliding window used when measuring window quality (default: 250)

- **--verbose**

  verbose output to stderr with info for each read

- **--version**

  display the program version and quit

- **-h**, **--help**

  display this help menu

For more information, go to: https://github.com/rrwick/Filtlong

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.