ANFO(1)

📦 version 0.98, in ubuntu jammy

✨ NAME ✨

okay bestie, meet anfo 🧚, the tool that finds the best alignment of short reads to a database 💖

anfo - find best alignment of short reads to database

📜 SYNOPSIS 📜

anfo [ option | file ... ]

💫 DESCRIPTION 💫

okay so anfo takes (short) sequencing reads and lines them up against a (gigabase sized) database 🧬 it's giving big data energy ✨ It starts with a heuristic seeding method, and then brings in a genuine aligner that allows gaps, understands damage patterns in ancient DNA, and spits out a score that's actually easy to interpret 💅

Input files can be any variety of FastA or FastQ files, or a native anfo binary file, optionally compressed using gzip or bzip2 🎀 The file format is automatically recognized, and other formats may be added later 🌈

🎀 OPTIONS 🎀

  • -V, --version — prints the version number and then exits, no drama 💖
  • -o file, --output file — writes your output to file. The file gets saved in the native anfo binary format, which you can work with using anfo-tool or the bindings to guile 🦋
  • -c conffile, --config conffile — reads your configuration from conffile. This is where you choose which indices get used (and by extension which genomes your alignment hits), tweak the aligner's parameters, and set paths 🗺️ check the example file if you're lost 🫶
  • -p num, --threads num — starts num threads for alignment. Honestly, one thread per processor core is usually the move 💪
  • -x num, --ixthreads num — starts num threads for indexing. Indexing uses less CPU than alignment, so having fewer indexers than aligners is usually the vibe 🌸
  • --solexa-scale — when reading FastQ files, this uses the Solexa scale (log-odds-ratios) instead of the standard Phred scale (probabilities). If you use Solexa/Illumina sequencers, check your documentation to see whether you need it. If you don't use them, you don't need it 🙈
  • --fastq-origin ori — sets the origin for FastQ decoding to ori. The standard and default is 33, but some versions of the Solexa/Illumina software need it set to 64 😭 Same deal: if you use Solexa/Illumina sequencers, check your docs. Otherwise, you're good 💅
  • -q, --quiet — suppresses all output except fatal errors. Shh 🤫
  • -v, --verbose — prints a progress indicator while things are running 🔥

🌸 ENVIRONMENT 🌸

  • ANFO_PATH — a colon-separated list of directories that gets searched for genome and index files 🗂️

📁 FILES 📁

  • /etc/popt — the system-wide configuration file for popt(3). anfo introduces itself to popt as "anfo" 🧁
  • ~/.popt — the per-user configuration file for popt(3) 👑
  • /usr/share/doc/anfo/example/*.cfg — example configuration files you can use with anfo 📚

🙈 BUGS 🙈

None known. Literally a clean slate 🥹✨

👑 AUTHOR 👑

Udo Stenzel <udo_stenzel@eva.mpg.de> 💜

🔗 SEE ALSO 🔗

Pulled from the Applications docs, dated OCTOBER 2009, manual page ANFO(1) 💖 stay iconic, bestie 🫶💅

📦 where this page comes from