KLEBORATE(1)

💖 KLEBORATE — the kleborate(1) page, bestie edition 💖

okay so real talk, this is the manual for kleborate, a user command, and it's literally the tool that screens Klebsiella genome assemblies. no cap. it's giving bioinformatics main character energy and i'm obsessed. 🦋

✨ NAME ✨

kleborate — the tool to screen Klebsiella genome assemblies 💅

🌸 SYNOPSIS 🌸

kleborate -a ASSEMBLIES [ASSEMBLIES ...] [-r] [-s] [--kaptive_k]
[--kaptive_o] [-k] [--all] [-o OUTFILE] [--kaptive_k_outfile
KAPTIVE_K_OUTFILE] [--kaptive_o_outfile KAPTIVE_O_OUTFILE] [-h]
[--version]

🎀 DESCRIPTION 🎀

Kleborate: a tool for characterising virulence and resistance in Klebsiella. periodt. that's the whole vibe. ✨

👑 OPTIONS 👑

💜 Required arguments (yes bestie, you have to)

• -a ASSEMBLIES [ASSEMBLIES ...], --assemblies ASSEMBLIES [ASSEMBLIES ...] — the FASTA file(s) for your assemblies. this one's mandatory, no skipping it 🙈

🌈 Screening options (pick your fighters)

• -r, --resistance — turns ON the resistance genes screening. (default: no resistance gene screening, so it's off unless you say so)
• -s, --species — turns ON Klebsiella species identification. heads up: this one requires Mash. (default: no species identification)
• --kaptive_k — turns ON Kaptive screening of K loci. (default: do not run Kaptive for K loci)
• --kaptive_o — turns ON Kaptive screening of O loci. (default: do not run Kaptive for O loci)
• -k, --kaptive — literally equivalent to --kaptive_k --kaptive_o. two for the price of one, slay 💅
• --all — equivalent to --resistance --species --kaptive. the "i want everything" button 🔥

🍓 Output options (where does the tea get written)

• -o OUTFILE, --outfile OUTFILE — the file for detailed output. (default: Kleborate_results.txt)
• --kaptive_k_outfile KAPTIVE_K_OUTFILE — the file for the full Kaptive K locus output. (default: do not save Kaptive K locus results to a separate file)
• --kaptive_o_outfile KAPTIVE_O_OUTFILE — the file for the full Kaptive O locus output. (default: do not save Kaptive O locus results to a separate file)

🧚 Help (we all need it sometimes)

• -h, --help — shows this help message and exits. bye bestie 🫶
• --version — shows the program's version number and exits. ⭐

🦋 AUTHOR 🦋

this manpage was written by Andreas Tille for the Debian distribution, and can be used for any other usage of the program. iconic of him honestly. 💖

and that's the whole page, babe ✨ kleborate 0.3.0, dated September 2019 — go characterise some virulence and resistance, you absolute legend 👑💅🌸