SIMKACOUNT(1)

✨ NAME ✨

simkaCount — a comparative metagenomics method dedicated to NGS datasets 🧬💖

🎀 SYNOPSIS 🎀

ok so bestie, here's the thing: this page doesn't actually give you a tidy synopsis line. What it gives you is the whole vibe of running the thing wrong, which honestly? iconic.

ERROR: Unknown parameter '-h'
ERROR: Option '-out-tmp-simka' is mandatory
ERROR: Option '-bank-name' is mandatory
ERROR: Option '-bank-index' is mandatory
ERROR: Option '-min-read-size' is mandatory
ERROR: Option '-min-shannon-index' is mandatory
ERROR: Option '-max-reads' is mandatory
ERROR: Option '-nb-datasets' is mandatory
ERROR: Option '-nb-partitions' is mandatory
ERROR: Option '-in' is mandatory

That's it. That's the whole DESCRIPTION up top. 💀

🌸 DESCRIPTION 🌸

So when you poke at this thing with -h, it does not hand you a cozy little help screen. Instead it yells at you with the block above — one ERROR: Unknown parameter '-h' and then a whole list of ERROR: Option '...' is mandatory lines for every option you forgot.

Translate it for me, bestie? Sure: that error list is literally the receipt of everything simkaCount needs before it'll even look at your data. Nine options are flagged mandatory here:

• -out-tmp-simka
• -bank-name
• -bank-index
• -min-read-size
• -min-shannon-index
• -max-reads
• -nb-datasets
• -nb-partitions
• -in

Not me reading a whole manpage and the manual page's DESCRIPTION is just a crash report. 🙈 Anyway. Below is the actual goods.

💅 [SimkaCount options] 💅

• -nb-cores (1 arg) — number of cores. [default '0']
• -verbose (1 arg) — verbosity level. [default '1']
• -version (0 arg) — version. zero args, she just tells you who she is. 💁
• -help (0 arg) — help. zero args again. (see the DESCRIPTION above for how that goes 💀)
• -out-tmp-simka (1 arg) — tmp output.
• -bank-name (1 arg) — bank name.
• -bank-index (1 arg) — bank name.
• -min-read-size (1 arg) — bank name.
• -min-shannon-index (1 arg) — bank name.
• -max-reads (1 arg) — bank name.
• -nb-datasets (1 arg) — bank name.
• -nb-partitions (1 arg) — bank name.
• -in (1 arg) — reads file.
• -kmer-size (1 arg) — size of a kmer. [default '31']
• -abundance-min (1 arg) — min abundance threshold for solid kmers. [default '0']
• -abundance-max (1 arg) — max abundance threshold for solid kmers. [default '2147483647']
• -abundance-min-threshold (1 arg) — min abundance hard threshold (only used when min abundance is "auto"). [default '2']
• -histo-max (1 arg) — max number of values in kmers histogram. [default '10000']
• -solidity-kind (1 arg) — way to compute counts of several files (sum, min, max, one, all, custom). [default 'sum']
• -solidity-custom (1 arg) — when solidity-kind is custom, specifies list of files where kmer must be present. [default '']
• -max-memory (1 arg) — max memory (in MBytes). [default '5000']
• -max-disk (1 arg) — max disk (in MBytes). [default '0']
• -solid-kmers-out (1 arg) — output file for solid kmers (only when constructing a graph). [default '']
• -out (1 arg) — output file. [default '']
• -out-dir (1 arg) — output directory. [default '.']
• -out-tmp (1 arg) — output directory for temporary files. [default '.']
• -out-compress (1 arg) — h5 compression level (0:none, 9:best). [default '0']
• -storage-type (1 arg) — storage type of kmer counts ('hdf5' or 'file'). [default 'hdf5']
• -histo2D (1 arg) — compute the 2D histogram (with first file = genome, remaining files = reads). [default '0']
• -histo (1 arg) — output the kmer abundance histogram. [default '0']

ngl the descriptions for -bank-index, -min-read-size, -min-shannon-index, -max-reads, -nb-datasets and -nb-partitions all just say "bank name" in the source. That's not me being lazy, that's genuinely what it says. Copying it exactly, periodt. 🫶

🔥 [kmer count, advanced performance tweaks options] 🔥

these are the spicy ones, for when you want to tune her. 🧚

• -minimizer-type (1 arg) — minimizer type (0=lexi, 1=freq). [default '0']
• -minimizer-size (1 arg) — size of a minimizer. [default '10']
• -repartition-type (1 arg) — minimizer repartition (0=unordered, 1=ordered). [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.

ok that's the whole page bestie, you're officially a simkaCount girlie now 💅🦋

simkaCount 1.5.1 · September 2019 — that's the version and date signing off, mwah 💖 go count some kmers, you've got this 🌸✨