KMC_TOOLS(1)

💖 kmc_tools(1) — the manual page, but make it make sense 💖

okay bestie, sit down, hydrate, and let me tell you about kmc_tools 🫶 this is the KMC_TOOLS(1) manual page and by the end of it you're gonna be running k-mer database ops like it's nothing. no cap.

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✨ NAME ✨

kmc_tools — extra operations you can do on k-mer databases 💅

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✨ SYNOPSIS ✨

kmc_tools [global parameters] <operation> [operation parameters]

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✨ DESCRIPTION ✨

So like… this command, and all its lil subcommands, implement a whole bunch of operations you can run on KMC databases. That's the whole vibe. ✨

🦋 k-mers sets operations for 2 KMC databases

these ones take two databases and do stuff with both of them, periodt:

• intersect — gives you the intersection of 2 k-mers sets 🔥
• kmers_subtract — subtraction of 2 k-mers sets
• counters_subtract — counters subtraction of 2 k-mer sets (yes it's different from the one above, iykyk)
• union — union of 2 k-mers sets 💖

🦋 operations for a single kmc database

one database, one main character, lots of options:

• sort — sorts the k-mers from a database generated by KMC2.x
• reduce — throws out the too-rare AND the too-frequent k-mers (bye to both extremes ✌️)
• compact — removes the counters, so you're storing only k-mers
• histogram — a histogram of k-mers occurrences 📊
• dump — dumps k-mers and counters out to a text file

🦋 more complex operations:

• complex — complex operations with a number of input databases (yes the name is honest, it's giving ✨ambitious✨)

🦋 other operations:

• filter — filters out reads that have too small a number of k-mers

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✨ OPTIONS ✨

global parameters:

• -t<value> — total number of threads (default: the number of CPU cores, so it just uses everything you got 👑)
• -v — enable verbose mode, which shows some information (default: false)
• -hp — hide the percentage progress (default: false) 🙈

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✨ EXAMPLE ✨

here's the moment you've been waiting for, an actual command, go off:

kmc_tools union db1 -ci3 db2 -ci5 -cx300 db1_union_db2 -ci10

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✨ SEE ALSO ✨

go read these next, bestie, they're all linked:

• kmc(1)
• kmc_tools-histogram(1)
• kmc_tools-compact(1)
• kmc_tools-intersect(1)
• kmc_tools-complex(1)
• kmc_tools-kmers_subtract(1)
• kmc_tools-counters_subtract(1)
• kmc_tools-sort(1)
• kmc_tools-dump(1)
• kmc_tools-union(1)
• kmc_tools-filter(1)

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✨ AUTHOR ✨

KMC was originally written by:

• Sebastian Deorowicz (sebastian.deorowicz@polsl.pl)
• Marek Kokot
• Szymon Grabowski
• Agnieszka Debudaj-Grabysz

icons, all of them, no notes 💅

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✨ COPYING ✨

KMC is free software distributed under the GNU GPL3 licence, and it's for academic, research, AND commercial use — so yes, you can use it for the bag too 💰

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and that's the whole page bestie!! 🎀 this was the KMC_TOOLS(1) manual, mwah, go union some databases 🌸💖