FASTQ-JOIN(1)

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

✨ NAME ✨

okay so hi bestie 💖 this is fastq-join(1), and it's part of ea-utils. what does it do? it joins two paired-end reads on the overlapping ends. that's the whole name, no cap. periodt. ✨

🌈 SYNOPSIS 🌈

fastq-join [options] <read1.fq> <read2.fq> [mate.fq] -o <read.%.fq>

💅 DESCRIPTION 💅

first, the original page literally has this line and we are keeping it because facts are facts, okay? 🫶

fastq-join: invalid option -- 'h' Unknown option `-h'.

then the actual description, and it's giving exactly what it says on the tin: it joins two paired-end reads on the overlapping ends. that's it. iconic. main character energy fr fr. 💅

🎀 OPTIONS 🎀

  • -o FIL — see the Output section below for the full tea on this one. 🍵
  • -v C — verifies that the 2 files probe id's match up to char C. (yes, "id's" with the apostrophe, that's literally what it says.) for Illumina reads, use ' ' (a space) for C. ✨
  • -p N — N-percent maximum difference (8). lowkey important, bestie.
  • -m N — N-minimum overlap (6). highkey also important.
  • -r FIL — verbose stitch length report. slay.
  • -R — no reverse complement. okayyy.
  • -x — allow insert < read length. noted. 💖

🌸 Output 🌸

  • you can supply 3 -o arguments, for un1, un2, join files, or one argument as a file name template. the suffix 'un1, un2, or join' is appended to the file, or they replace a %-character if present. iykyk.
  • if a 'mate' input file is present (barcode read), then the files 'un3' and 'join2' are also created. the way that this just works? obsessed. 🦋

and that's the tea! this page is from fastq-join 1.1.2, dated July 2015. love u, bye 💋

📦 where this page comes from