SIMKAMIN(1)

📦 version 1.5.3, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

🦋 NAME

simkaMin — a comparative metagenomics method dedicated to NGS datasets ✨

✨ DESCRIPTION ✨

okay bestie so real talk: simkaMin is a whole comparative metagenomics moment, made specifically for NGS datasets. it's giving "I compare your metagenomes and I do it beautifully." let's get into the flags, because there are a lot and we're covering every single one, no skips 💅

💖 [main options]

the main-character flags. the ones you literally cannot skip.

  • -in (1 arg) — the input file of datasets 🫶 one sample per line, formatted like id1: filename1...
  • -out (1 arg) — the output directory for result files (aka the distance matrices). [Default: ./simka_results]
  • -seed (1 arg) — the seed used for random k-mer selection. [Default: 100]
  • -bin (1 arg) — the path to the simkaMinCore program. specify this if it's not in your PATH, or not sitting in the standard installation directory <simkaDir>/build/bin/simkaMinCore 🌸

🧚 [core options]

the engine-room vibes. how much power you're handing over.

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

🎀 [k-mer options]

k-mer girlies rise up, this section is ours.

  • -kmer-size (1 arg) — size of a kmer. [Default: 21]
  • -nb-kmers (1 arg) — number of kmers used to compute distances. [Default: 1000000]
  • -filter (0 arg) — filter out k-mer seen one time (potentially erroneous). lowkey a cleanup slay 🧹

🌈 [read options]

the read-handling rules. setting boundaries, as you should.

  • -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. 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. periodt 💜

and that's the whole page bestie!! this is simkaMin 1.5.1 from September 2019, filed under SIMKAMIN(1) in the User Commands section of the manual. go forth and compare those metagenomes, you absolute icon 🦋✨💖

📦 where this page comes from