RAGOUT(1)

💖 RAGOUT(1) — like, the manual page for ragout, bestie 💖

okay so this is the user-commands page for ragout — chromosome assembly with multiple references ✨ (yes the section is literally called NAME, and that's the whole vibe).

✨ SYNOPSIS ✨

no cap, here's exactly how you call her:

ragout [-h] [-o output_dir] [-s {sibelia,maf,hal}] [--refine]
[--solid-scaffolds] [--overwrite] [--repeats] [--debug] [-t THREADS]
[--version] recipe_file

🎀 OPTIONS 🎀

🌸 positional arguments:

• recipe_file — the path to your recipe file, like the little list of ingredients that tells ragout what's going on 🍓

💅 optional arguments:

• -h, --help — shows this help message and then dips. iconic behaviour honestly.
• -o output_dir, --outdir output_dir — where the results go. default: ragout-out 💖
• -s {sibelia,maf,hal}, --synteny {sibelia,maf,hal} — picks the backend for synteny block decomposition. default: sibelia ✨
• --refine — turns on refinement with the assembly graph. default: False
• --solid-scaffolds — does not break input sequences — this disables the chimera detection module. default: False
• --overwrite — overwrites the results from the previous run, so like, no take-backs. default: False
• --repeats — enables the repeat resolution algorithm. default: False 🔁
• --debug — enables debug output. default: False
• -t THREADS, --threads THREADS — number of threads for the synteny backend. default: 1 👑
• --version — shows the program's version number and exits. bye bestie 👋

🦋 AUTHOR 🦋

This manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program. 🫶

and that's the whole page, periodt 💅 this was ragout version 2.1.1, from February 2019 — mwah, go assemble some chromosomes, you main character 🌈⭐