---
name: "NanoFilt"
section: "1"
platform: "linux"
package: "nanofilt"
version: "2.8.0-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/NanoFilt"
---

# NanoFilt(1)

filtering and trimming of long read sequencing data

## NAME

NanoFilt - filtering and trimming of long read sequencing data

## DESCRIPTION

usage: NanoFilt \[-h\] \[-v\] \[--logfile LOGFILE\] \[-l LENGTH\]

-

  \[--maxlength MAXLENGTH\] \[-q QUALITY\] \[--minGC MINGC\] \[--maxGC MAXGC\] \[--headcrop HEADCROP\] \[--tailcrop TAILCROP\] \[-s SUMMARY\] \[--readtype {1D,2D,1D2}\] \[input\]

Perform quality and/or length and/or GC filtering of (long read) fastq data.           Reads on stdin.

### General options:

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

  show the help and exit

- **-v**, **--version**

  Print version and exit.

- **--logfile** LOGFILE

  Specify the path and filename for the log file.

- input

  input, uncompressed fastq file

### Options for filtering reads on.:

- **-l** LENGTH, **--length** LENGTH

  Filter on a minimum read length

- **--maxlength** MAXLENGTH

  Filter on a maximum read length

- **-q** QUALITY, **--quality** QUALITY

  Filter on a minimum average read quality score

- **--minGC** MINGC

  Sequences must have GC content \>= to this. Float between 0.0 and 1.0. Ignored if using summary file.

- **--maxGC** MAXGC

  Sequences must have GC content \<= to this. Float between 0.0 and 1.0. Ignored if using summary file.

### Options for trimming reads.:

- **--headcrop** HEADCROP

  Trim n nucleotides from start of read

- **--tailcrop** TAILCROP

  Trim n nucleotides from end of read

### Input options.:

- **-s** SUMMARY, **--summary** SUMMARY

  Use albacore or guppy summary file for quality scores

- **--readtype** {1D,2D,1D2}

  Which read type to extract information about from summary. Options are 1D, 2D or 1D2

### EXAMPLES:

-

  gunzip **-c** reads.fastq.gz \| NanoFilt **-q** 10 **-l** 500 **--headcrop** 50 \| minimap2 genome.fa - \| samtools sort **-O** BAM -@24 **-o** alignment.bam - gunzip **-c** reads.fastq.gz \| NanoFilt **-q** 12 **--headcrop** 75 \| gzip \> trimmed-reads.fastq.gz gunzip **-c** reads.fastq.gz \| NanoFilt **-q** 10 \| gzip \> highQuality-reads.fastq.gz

## SEE ALSO

The full documentation for **NanoFilt** is maintained as a Texinfo manual.  If the **info** and **NanoFilt** programs are properly installed at your site, the command

-

  **info NanoFilt**

should give you access to the complete manual.