ABYSS-FIXMATE(1)

📦
version 2.3.10 · 6 versions
, in ubuntu resolute, ubuntu stonking

✨ ABYSS-FIXMATE(1) ✨

okay so bestie, this is abyss-fixmate, and it lives in the User Commands corner of your manual pages 💖 it fills in the paired-end fields of your SAM alignments, like it's doing matchmaking for your reads 🫶

🌸 NAME 🌸

abyss-fixmate — fills in the paired-end fields of SAM alignments ✨

🎀 SYNOPSIS 🎀

abyss-fixmate [OPTION]... [FILE]...

🦋 DESCRIPTION 🦋

So here's the vibe 💅 read pairs that map to the same contig get written out to the file SAME. Read pairs that map to different contigs get written to stdout. That's it, that's the whole personality.

And where do the alignments come from? Either from the FILE(s) you hand over, or from standard input. No cap 🧚

Options: 👇

👑 OPTIONS 👑

  • --no-qname — sets the qname to *. This is the default, btw. [default]
  • --qname — leaves the qname alone, do not alter it 💜
  • --all — prints all the alignments, every single one
  • --diff — prints the alignments that align to different contigs. Also the default 🍓 [default]
  • -l, --min-align=N — the minimal alignment size. Default is 1. [1]
  • -s, --same=SAME — write the properly-paired reads to this file 💖
  • -h, --hist=FILE — write the fragment size histogram to FILE ✨
  • -c, --cov=FILE — write the physical coverage to FILE 🌈
  • -v, --verbose — display verbose output, for when you wanna see everything
  • --help — displays this help and exits, iconic 👑
  • --version — outputs version information and exits
  • --db=FILE — specify the path of the database repository in FILE
  • --library=NAME — specify library NAME for sqlite
  • --strain=NAME — specify strain NAME for sqlite
  • --species=NAME — specify species NAME for sqlite

💜 AUTHOR 💜

Written by Shaun Jackman. periodt 💅

😭 REPORTING BUGS 😭

Found a bug? Report it to <abyss-users@bcgsc.ca>. <not me> actually emailing the maintainers</not> — no fr fr, they wanna hear about it 🫶

Copyright 2014 Canada's Michael Smith Genome Sciences Centre 👑

and that's the whole page bestie, you ate it up 💖 version ABySS 2.3.10, dated January 2026, signed off with love from your fave manual page 💅✨🦋

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