FASTQ-STATS(1)

📦 version 1.1.2, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 FASTQ-STATS — bestie edition 💖

okay so this is fastq-stats, and it lives in the User Commands section of the manual. yes, the lowercase-with-a-dash girlies, we love her. 🌸

✨ NAME ✨

fastq-stats — part of ea-utils, and it produces lots of easily digested statistics. that's literally the whole job description and honestly? iconic. 💅

🦋 SYNOPSIS 🦋

fastq-stats [options] <fastq-file>

👑 DESCRIPTION 👑

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

it produces lots of easily digested statistics for the files listed. no cap, that's it, that's the mission. 🫶

🎀 Options 🎀

  • -c — cyclemax: max cycles for which the following quality stats are produced. default is [35].
  • -w INT — window: max window size for generating duplicate read statistics. default is [2000000].
  • -d — debug: prints out debug statements.
  • -D — don't do duplicate read statistics. (yes, capital D. they're different options bestie, don't mix them up 😭)
  • -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.
lowkey the move here is: run it, read the stats, feel like the main character of your own sequencing run. 🧚

mwah, that's a wrap! this lil page is fastq-stats 1.1.2, dated July 2015, and it came to you straight from the User Commands corner of the manual. go forth and count those bases, bestie 💜🍓✨

📦 where this page comes from