SIMKAMIN_UPDATE(1)

✨ SIMKAMIN_UPDATE(1) ✨

okay bestie, so this is simkaMin_update from the User Commands manual section, and it's literally the comparative metagenomics method dedicated to NGS datasets 💖 like that's the whole vibe, that's the name, periodt.

🎀 NAME 🎀

simkaMin_update — a comparative metagenomics method dedicated to NGS datasets 🦋

🌸 DESCRIPTION 🌸

So here's the tea: simkaMin_update is the girl who shows up to update your existing results. Let's get into it, sub-section by sub-section, no skips, no cap 🔥

💅 [main options]

• -in (1 arg) — the input file of datasets, aka the datasets you wanna add to existing simka results 🫶
• -in-to-update (1 arg) — path to the existing simka results you want to update. heads up bestie: existing results will be overwritten 💀 like, gone. replaced. iconic but also be careful.
• -bin (1 arg) — path to the simkaMinCore program. you only gotta specify this if it's not in PATH, or not chillin' in the standard installation directory which is <simkaDir>/build/bin/simkaMinCore 🌈

⚙️ [core options]

• -nb-cores (1 arg) — number of cores. [Default: 0] ⭐
• -max-memory (1 arg) — max memory in MB. [Default: 8000] 🧚

🧬 [k-mer options]

• -filter (0 arg) — filter out k-mer seen one time, 'cause it's potentially erroneous 👀 (this one takes no arg, she just is)

📖 [read options]

• -max-reads (1 arg) — maximum number of reads per sample to process. [Default: 0] 🌸
• -min-read-size (1 arg) — minimal size a read should have to be kept. [Default: 0] 💜
• -min-shannon-index (1 arg) — minimal Shannon index a read should have to be kept. it's a Float in [0,2]. [Default: 0] ✨

👑 AUTHOR 👑

This manpage was written by Shayan Doust for the Debian distribution and can be used for any other usage of the program. slay 💅

and that's the whole thing bestie, every flag, every default, nothing skipped 🫶

kisses, this was simkaMin_update version 1.5.1, dated September 2019 🌈⭐💖