ABYSS(1)

📦 version 2.3.1, in ubuntu jammy

🌊 ABYSS(1) 🌊

okay bestie, this is the manual page for ABYSS, filed under User Commands 💅 let's get into it!

✨ NAME ✨

ABYSS - assemble short reads into contigs 🧚

💖 SYNOPSIS 💖

ABYSS [OPTION]... FILE...

📖 DESCRIPTION 📖

so the whole vibe is that ABYSS assembles all your input files, FILE, and they can be in FASTA, FASTQ, qseq, export, SRA, SAM or BAM format 🍓 they can also be compressed with gz, bz2 or xz, and they can even be tarred. literally so flexible 😭

ngl, if you want to run a full assembly with ABySS, the move is to use abyss-pe as your entry point instead of the ABYSS program 👑 abyss-pe is a Makefile that coordinates a bunch of the ABySS tools (ABYSS included) to run the whole ABySS assembly pipeline. it can do stuff ABYSS can't, like leveraging the distance info from paired end reads and mate pair reads 🦋

here are all the options, no skipping 💅

  • --chastity — discard unchaste reads [default] 🌸
  • --no-chastity — do not discard unchaste reads 🙈
  • --trim-masked — trim masked bases from the ends of reads [default] ✨
  • --no-trim-masked — do not trim masked bases from the ends of reads 💜
  • -q, --trim-quality=THRESHOLD — trim bases from the ends of reads whose quality is less than the threshold 🎀
  • -Q, --mask-quality=THRESHOLD — mask all bases in reads whose quality is less than the threshold 🫶
  • --standard-quality — zero quality is !' (33). default for FASTQ and SAM files 🌈
  • --illumina-quality — zero quality is @' (64). default for qseq and export files 🦋
  • -o, --out=FILE — write the contigs to FILE 🍓
  • -k, --kmer=KMER_SIZE — k-mer size 🔥
  • -t, --trim-length=TRIM_LENGTH — maximum length of dangling edges to trim ✂️
  • -c, --coverage=COVERAGE — remove contigs with mean k-mer coverage less than this threshold 🧹
  • -b, --bubbles=N — pop bubbles shorter than N bp (default: 3*k). bubble popping, iconic 🫧
  • -b0, --no-bubbles — do not pop bubbles 🙅‍♀️
  • -e, --erode=COVERAGE — erode bases at the ends of blunt contigs with coverage less than this threshold 💧
  • -E, --erode-strand=COVERAGE — erode bases at the ends of blunt contigs with coverage less than this threshold on either strand 🌊
  • --coverage-hist=FILE — record the k-mer coverage histogram in FILE 📊
  • -g, --graph=FILE — generate a graph in dot format 🕸️
  • -s, --snp=FILE — record popped bubbles in FILE 🧾
  • -v, --verbose — display verbose output 📣
  • --help — display this help and exit 🆘
  • --version — output version information and exit 🏷️

🎀 AUTHOR 🎀

Written by Jared Simpson and Shaun Jackman. 👩‍💻✨

🐛 REPORTING BUGS 🐛

Report bugs to <abyss-users@bcgsc.ca>. 🚨

Copyright 2015 Canada's Michael Smith Genome Sciences Centre 🇨🇦🌸

and that's the whole page, bestie 🫶 this one is from ABYSS (ABySS) 2.3.1, dated 2015-May. go forth and assemble responsibly 💅✨

📦 where this page comes from