RAMBO-K(1)

💖 RAMBO-K(1) 💖

okay bestie, pull up a chair, we're reading the rambo-k manual page together and honestly? it's giving main character energy for bioinformatics. it lives in the User Commands section of the manual, so you already know it's something you run, not something you read like a novel. 🦋

✨ NAME ✨

rambo-k — Read Assignment Method Based On K-mers 💅

(that acronym ate, fr fr)

🌸 SYNOPSIS 🌸

rambo-k [-h] -r REFFILE1 -R REFFILE2 [-n NAME1] [-N NAME2] -1
UNASSIGNED1 [-2 UNASSIGNED2] [-k KMERSIZES] [-o OUTPATH] [-a AMOUNT] [-t
THREADS] [-x CHUNKSIZE] [-g GAPSIZE] [-c CUTOFF_LOWER] [-C
CUTOFF_HIGHER] [-d] [-f FILETYPE]

no cap, that's a lot of brackets. the un-bracketed ones are the mandatory besties (-r, -R, -1), everything else is optional garnish. 🌈

👑 DESCRIPTION 👑

so like. RAMBO-K is a reference-based tool that does rapid and sensitive extraction of one organism's reads out of a mixed dataset. it's built on a Markov chain implementation, which uses the genomic characteristics of each reference to assign reads to the associated set. 🧬✨

translation: you give it two references, it goes through your messy mixed reads and sorts out who belongs to whom. iconic behavior.

🎀 OPTIONS 🎀

every single flag, coming right up, no skipping:

• -h, --help — show this help message and exit. the classic escape hatch, we love her. 🫶
• -r REFFILE1, --reffile1 REFFILE1 — Reference file of species 1, in fasta-format. should pair with name1. 🍓
• -R REFFILE2, --reffile2 REFFILE2 — Reference file of species 2, in fasta-format. should pair with name2. 🍓
• -n NAME1, --name1 NAME1 — Name of species 1. yes it's just a name. name your species, bestie. 💖
• -N NAME2, --name2 NAME2 — Name of species 2. also a name. symmetrical, as it should be. 💖
• -1 UNASSIGNED1, --unassigned1 UNASSIGNED1 — Fasta- or fastq-file containing mixed reads. this is the chaotic pile of reads you want sorted. 🌀
• -2 UNASSIGNED2, --unassigned2 UNASSIGNED2 — Fasta- or fastq-file containing mixed reads, only required in paired end mode. so if you're not doing paired end, she's not needed, periodt. ✌️
• -k KMERSIZES, --kmersizes KMERSIZES — Order of Markov-Chain/kmer length. enter as a range (e.g. 4:8) or a list (e.g. 4,6,8) or a single integer (e.g. 8). Default = 8. so many ways to say the same thing and honestly? we respect the flexibility. 🔥
• -o OUTPATH, --outpath OUTPATH — Folder to write results to. Default = $name1_$name2/ in your working directory. it literally names the folder after your two species, cute. 🎀
• -a AMOUNT, --amount AMOUNT — Number of reads to be simulated, default = 50000. the simulation girlies stay busy. ✨
• -t THREADS, --threads THREADS — Number of Threads to use. throw more cores at it, go off. 💅
• -x CHUNKSIZE, --chunksize CHUNKSIZE — Size of chunks created at a time for simulation, default = 100000.

⚠️ Only change if you know what you are doing! like genuinely, bestie, don't touch the knobs if you don't know what the knobs do. 🙈

• -g GAPSIZE, --gapsize GAPSIZE — Estimated size of gapsize in case of paired end reads, default = 1. 🦋
• -c CUTOFF_LOWER, --cutoff_lower CUTOFF_LOWER — Lower cutoff: output only reads with a score lower than or equal to this value, use m1 for -1. 📉
• -C CUTOFF_HIGHER, --cutoff_higher CUTOFF_HIGHER — Higher cutoff: output only reads with a score higher than or equal to this value, use m1 for -1. 📈
• -d, --delete_temp — Delete temporary files. Calculations will start from beginning next time. so, like, clean slate energy — but also, you're redoing the work next time, so know what you're signing up for. 💀
• -f FILETYPE, --filetype FILETYPE — Type of your input reads. fasta or fastq, default = fastq. pick your format, pick your fighter. 🥊

🌟 AUTHOR 🌟

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. shoutout Andreas, an absolute legend. 👑

and that's the whole page, bestie! 💜 this little doc is for rambo-k version 1.21, dated November 2016 — yes, she's vintage, and she still slays. go extract some reads, you've got this. 🌸✨🫶