POLISH_CLUSTERS(1)

💖 POLISH_CLUSTERS 💖

okay bestie, welcome to the polish_clusters(1) manual page — yes that's the section 1, user commands, we're in the big leagues now 👑

✨ NAME ✨

polish_clusters — a whole lil collection of tools that annotate genomes using long read transcriptomics data 🧬🦋

🌸 DESCRIPTION 🌸

🎀 Usage of polish_clusters 🎀

so like, here's the vibe — this is how you call it, and here is every single flag it takes. no notes, no skips, we're doing all of them 💅

• -V — prints out the version. quick lil flex, tells you what you're running ✨
• -a string — read cluster memberships in tabular format. that's the input, bestie, hand it over 🫶
• -c int — minimum cluster size. (default 1) tiny clusters need not apply 🙈
• -d string — location of the temporary directory. where the chaos happens behind the scenes 🌀
• -h — print out the help message. the classic "wait what do I do" button 😭
• -m — do not load all reads in memory (slower). yes it's slower, no we're not sugarcoating it, it's literally in the docs — it trades speed for RAM and that's the whole deal 💀
• -o string — output fasta file. your final product, the main character output 👑
• -t int — number of cores to use. (default 4) go ahead and give it more, she's hungry 🔥
• -x string — arguments passed to minimap2. whatever you put here gets handed straight over, no middleman 🌈
• -y string — arguments passed to racon. same deal, straight through, exactly as you wrote it ⭐

ngl, -x and -y are just lil relay batons — polish_clusters doesn't interpret them, it just passes them along, so whatever those tools accept is on you 🎀

💜 AUTHOR 💜

this manpage was written by Nilesh Patra for the Debian distribution, and it can be used for any other usage of the program. iconic behaviour, we love a flexible license moment 🫶✨

and that's the whole page, bestie 💖 this was polish_clusters version 0.1.0+ds, dated September 2020 — go annotate some genomes, you've got this 🌸🦋💅