FASTANI(1)

✨ fastANI(1) — the manual page, but make it slay ✨

okay bestie, welcome to fastANI(1), aka the User Commands section of the manual, aka the place where we learn how to compute ANI without losing our minds 💖

🌸 NAME 🌸

fastANI — fast alignment-free computation of whole-genome Average Nucleotide Identity. yes that's the whole name, and yes it's a mouthful, but it's iconic 🎀

💫 DESCRIPTION 💫

so like, fastANI is a fast, alignment-free implementation for computing whole-genome Average Nucleotide Identity (ANI) between genomes. no alignments, no drama, just vibes and numbers ✨

Example usage, literally copy-paste these:

$ fastANI -q genome1.fa -r genome2.fa -o output.txt
$ fastANI -q genome1.fa --rl genome_list.txt -o output.txt

👑 AVAILABLE OPTIONS 👑

one bullet per flag, bestie, we do not skip a single one 🫶

• -h, --help — prints this help page. the classic. the moment.
• -r <value>, --ref <value> — your reference genome, in fasta/fastq format, and yes [.gz] is allowed, gzipped girlies rise up 💅
• --refList <value>, --rl <value> — a file containing a list of reference genome files, one genome per line. a whole roster, basically 🌈
• -q <value>, --query <value> — your query genome, fasta/fastq, [.gz] friendly 🦋
• --ql <value>, --queryList <value> — a file containing a list of query genome files, one genome per line 🍓
• -k <value>, --kmer <value> — kmer size, and heads up: it must be <= 16 — [default : 16] ⭐
• -t <value>, --threads <value> — thread count for parallel execution, [default : 1]. bump it up if your machine is built different 🔥
• --fragLen <value> — fragment length, [default : 3,000] 💜
• --minFraction <value> — minimum fraction of genome that must be shared for trusting the ANI. if the reference and query genome sizes differ, the smaller one among the two is the one that counts. [default : 0.2] — so don't come for the ANI if the genomes barely overlap, ok? 🙈
• --visualize — outputs mappings for visualization. ngl this one can only be enabled for single genome to single genome comparison, so no group projects 💀 [disabled by default]
• --matrix — also outputs ANI values as a lower triangular matrix (format inspired from phylip). if you enable this, expect an output file with a .matrix extension, no cap 📐 [disabled by default]
• -o <value>, --output <value> — output file name. and listen — this one is [required], you literally cannot skip it, periodt 🚨
• -v, --version — shows the version 👑

💜 AUTHOR 💜

this manpage was written by Nilesh Patra for the Debian distribution, and it can be used for any other usage of the program. a legend, honestly 🌟

okay that's the whole page bestie, go compute some ANI 💖✨ this was fastANI 1.32, dated March 2021, signing off with main character energy 🎀🦋💅