KMC(1)

💖 KMC — the k-mer counter that ate 💖

okay bestie, listen up: this is the manual page for kmc, aka KMC, and it lives in section 1 of the manual. she counts k-mers. she's iconic. let's go 🧚✨

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✨ NAME ✨

kmc — count kmers in genomic sequences 💅

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🌸 DESCRIPTION 🌸

So KMC—K-mer Counter is this utility that's literally designed for counting k-mers — and by k-mers we mean sequences of consecutive k symbols — inside a set of reads from genome sequencing projects. that's it. that's the whole vibe. 🦋

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🎀 SYNOPSIS 🎀

kmc [options] <input_file_name> <output_file_name> <working_directory>

kmc [options] <@input_file_names> <output_file_name> <working_directory>

so yeah, you either hand her one input file, or you hit her with the @-list of input file names. either way she needs the output file name and a working directory. no cap. 👑

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💅 OPTIONS 💅

okay this is the part where you screenshot and save to your notes app, fr fr. every single one, no skips:

• -v — verbose mode, she shows you all the parameter settings. default: false (she's quiet by default, mysterious ✨)
• -k<len> — k-mer length, where k goes from 1 to 256; default: 25
• -m<size> — max amount of RAM in GB, from 1 to 1024; default: 12
• -sm — use strict memory mode, meaning the memory limit from the -m<n> switch will not be exceeded. she stays in her lane 🫶
• -hc — count homopolymer compressed k-mers (this one is approximate and experimental, so like… she's trying her best, be nice 🙈)
• -p<par> — signature length, one of 5, 6, 7, 8, 9, 10, 11; default: 9
• -f<a/q/m/bam/kmc> — what format is the input, bestie? FASTA format is -fa, FASTQ format is -fq, multi FASTA is -fm, or BAM via -fbam, or KMC via -fkmc; default: FASTQ
• -ci<value> — exclude k-mers occurring less than <value> times (default: 2)
• -cs<value> — maximal value of a counter (default: 255)
• -cx<value> — exclude k-mers occurring more of than <value> times (default: 1e9)
• -b — turn off transformation of k-mers into canonical form
• -r — turn on RAM-only mode
• -n<value> — number of bins
• -t<value> — total number of threads (default: no. of CPU cores — she'll use the whole squad 💀)
• -sf<value> — number of FASTQ reading threads
• -sp<value> — number of splitting threads
• -sr<value> — number of threads for 2nd stage
• -j<file_name> — file name with execution summary in JSON format
• -w — without output
• -o<kmc/kff> — output in KMC of KFF format; default: KMC
• -hp — hide percentage progress (default: false)
• -e — only estimate histogram of k-mers occurrences instead of doing exact k-mer counting
• --opt-out-size — optimize output database size (heads up: this may increase running time ⏳)

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🌈 EXAMPLES 🌈

the main character moments, copy these exactly bestie:

kmc -k27 -m24 NA19238.fastq NA.res /data/kmc_tmp_dir/

kmc -k27 -m24 @files.lst NA.res /data/kmc_tmp_dir/

first one: single fastq, k=27, 24 GB of RAM. second one: same energy but she's reading her file list from @files.lst. slay. 🔥

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👑 AUTHOR 👑

kmc was originally written by:

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

legends, honestly. 🫶

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⭐ COPYING ⭐

KMC is a free software distributed under the GNU GPL3 licence for academic, research, and commercial use. free is free, periodt. 💖

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ngl bestie if you got all the way down here you're officially a k-mer girlie now. iykyk 🌸

and that's the whole page — K-Mer Counter (KMC) ver. 3.2...., dated February 2024, straight out of the KMC(1) manual. mwah, go count some kmers 💅✨🎀