---
name: "fastq-stats"
section: "1"
platform: "linux"
package: "ea-utils"
version: "1.1.2+dfsg-9+b3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/fastq-stats"
---

# fastq-stats(1)

ea-utils: produce lots of easily digested statistics

## NAME

fastq-stats - ea-utils: produce lots of easily digested statistics

## SYNOPSIS

**fastq-stats** \[*options*\] *\<fastq-file\>*

## DESCRIPTION

Version: 1.01 $Id: fastq-stats.cpp 652 2013-09-17 17:40:32Z earonesty $

Produces lots of easily digested statistics for the files listed

Options

**-c**     cyclemax: max cycles for which following quality stats are produced \[35\] **-w** INT window: max window size for generating duplicate read statistics \[2000000\] **-d**     debug: prints out debug statements **-D**     don't do duplicate read statistics **-s** INT number of top duplicate reads to display **-x** FIL output fastx statistics (requires an output filename) **-b** FIL output base breakdown by per phred quality at every cycle.

-

  It sets cylemax to longest read length

**-L** FIL Output length counts

The following data are printed to stdout:

- reads

  : #reads in the fastq file

- len

  : read length. mean and stdev are provided for variable read lengths

- phred

  : phred scale used

- window-size

  : Number of reads used to generate duplicate read statistics

- cycle-max

  : Number of bases to assess for duplicity

- dups

  : Number of reads that are duplicates

- %dup

  : Pct reads that are duplcate

- unique-dup seq

  : Number sequences that are duplicated

- min dup count

  : Smallest duplicate tally for any duplicate sequence

- dup seq \<rank\> \<count\> \<sequence\>

  : Lists top 10 most frequent duplicate reads along with count mean and stdev

- qual

  : Base Quality min, max and mean

- %A,%T,%C,%G

  : base percentages

- total bases

  : total number of bases