SIMKA(1)

💖 NAME 💖

simka — a comparative metagenomics method dedicated to NGS datasets 🌈

(and yes bestie, you're on the SIMKA(1) page, section 1, User Commands — you found it 🫶)

✨ DESCRIPTION ✨

okay so first thing, bestie, do not come in here expecting -h to be all sweet and helpful. it is not. if you poke it with -h it literally just yells this at you:

ERROR: Unknown parameter '-h' ERROR: Option '-in' is mandatory ERROR: Option '-out-tmp' is mandatory ERROR: Option '-in' is mandatory

🚨 real talk: -in and -out-tmp are mandatory. -out-tmp has no default listed, so you have to hand it over yourself. skip either one and you get that exact yell up there. no notes.

💅 [Simka options] 💅

• -in (1 arg) — the input file of samples. one sample per line, and it goes id1: filename1...
• -out (1 arg) — output directory for the result files (the distance matrices) — [default './simka_results'] 🎀
• -out-tmp (1 arg) — output directory for the temporary files
• -keep-tmp (0 arg) — keep the temporary files (hoarder behavior, but valid)
• -data-info (0 arg) — compute (and display) information before running Simka, like the number of reads per dataset
• -verbose (1 arg) — verbosity level — [default '1']
• -version (0 arg) — version
• -help (0 arg) — help

🦋 [distance options] 🦋

• -simple-dist (0 arg) — compute all the simple distances (Chord, Hellinger...)
• -complex-dist (0 arg) — compute all the complex distances (Jensen-Shannon...)

🌸 [kmer options] 🌸

• -kmer-size (1 arg) — size of a kmer — [default '21']
• -abundance-min (1 arg) — min abundance a kmer need to be considered — [default '2']
• -abundance-max (1 arg) — max abundance a kmer can have to be considered — [default '999999999']
• -kmer-shannon-index (1 arg) — minimal Shannon index a kmer should have to be kept. Float in [0,2] — [default '0']

🍓 [read options] 🍓

• -max-reads (1 arg) — maximum number of reads per sample to process. Can be -1: use all reads. Can be 0: estimate it — [default '-1']
• -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']

💜 [core options] 💜

• -nb-cores (1 arg) — number of cores — [default '0']
• -max-memory (1 arg) — max memory (MB) — [default '5000']
• -max-count (1 arg) — maximum number of simultaneous counting jobs (a higher value improve execution time but increase temporary disk usage) — [default '']
• -max-merge (1 arg) — maximum number of simultaneous merging jobs (1 job = 1 core) — [default '']

🧚 [cluster options] 🧚

• -count-cmd (1 arg) — command to submit counting job — [default '']
• -merge-cmd (1 arg) — command to submit merging job — [default '']
• -count-file (1 arg) — filename to the couting job template — [default '']
• -merge-file (1 arg) — filename to the merging job template — [default '']

👑 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 page, bestie!! this one's simka version 1.5.1, dated September 2019, from the SIMKA(1) manual — go forth and compute those distances ✨🦋💖