KMC_TOOLS-FILTER(1)

💖 KMC_TOOLS-FILTER 💖

okay bestie, welcome to KMC_TOOLS-FILTER(1) — that's the section 1 manual page for the kmc_tools-filter command. grab a strawberry 🍓, we're filtering reads.

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✨ NAME ✨

kmc_tools-filter — filter out reads with too small number of k-mers 🧚

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✨ SYNOPSIS ✨

kmc_tools filter <kmc_input_db> [kmc_input_db_params] <input_read_set>
[input_read_set_params] <output_read_set> [output_read_set_params]

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✨ DESCRIPTION ✨

This command filters out reads with too small number of k-mers. that's it, that's the whole vibe. reads that are too k-mer-poor get yeeted 💅

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✨ OPTIONS ✨

for the k-mers database, there are additional parameters 🗂️

• -ci<value> — exclude k-mers occurring less than <value> times
• -cx<value> — exclude k-mers occurring more of than <value> times

for the input set of reads, there are additional parameters 🌸

• -ci<value> — remove reads containing less k-mers than value. It can be integer or floating number in range [0.0;1.0]
• -ci<value> — remove reads containing more k-mers than value. It can be integer or floating number in range [0.0;1.0]

not me pointing out that the page lists -ci<value> twice up there — yes, literally twice, we're just reporting what it says, no editing from me 🙈

• -f<a/q> — input in FASTA format (-fa), FASTQ format (-fq); default: FASTQ

for the output set of reads, there are additional parameters 🎀

• -f<a/q> — output in FASTA format (-fa), FASTQ format (-fq); default: same as input

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✨ EXAMPLE ✨

kmc_tools filter kmc_db -ci3 input.fastq -ci0.5 -cx1.0 filtered.fastq
kmc_tools filter kmc_db input.fastq -ci10 -cx100 filtered.fastq

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✨ AUTHOR ✨

KMC was originally written by:

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

the way that's a whole squad of authors 🔥 iconic.

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✨ COPYING ✨

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

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and that's a wrap, bestie 🫶 the footer is literally just KMC_TOOLS-FILTER(1) saying its own name again — section 1, same title, no extra date or version info hiding down there. slay, go filter something 💖✨🌈