KMC_TOOLS-INTERSECT(1)

💖 KMC_TOOLS-INTERSECT(1) 💖

okay so bestie, welcome to kmc_tools-intersect, one of the kmc_tools girlies 👑 this is the part of the KMC manual, and she's here to do one thing and do it iconically: find the k-mers that BOTH of your databases have in common. no cap.

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✨ NAME ✨

kmc_tools-intersect — calculate intersection of two KMC databases 🫶

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🌸 SYNOPSIS 🌸

kmc_tools intersect <input1 [input1_params]> <input2 [input2_params]>
<output [output_params]>

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🦋 DESCRIPTION 🦋

So the way that this works is: the output database is gonna contain only the k-mers that are present in both input sets. both. not one, not the other, BOTH. it's giving matched set energy 💅

and the counter value in the output database? it's equal to the lower counter value in the input. literally, whichever one is smaller, that's what you get. slay.

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🎀 OPTIONS 🎀

💜 For each input there are additional parameters:

• -ci<value> — exclude k-mers occurring less than <value> times. bye bye rare little guys 🙈
• -cx<value> — exclude k-mers occurring more of than <value> times. like, more of than. that's what it says. the overachievers get filtered out too 😭

🌈 For output 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
• -cs<value> — maximal value of a counter. the counter can't go higher than this, periodt ⭐

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🍓 EXAMPLE 🍓

here's the whole vibe, start to finish, copy it exactly bestie:

kmc -k28 file1.fastq kmers1 tmp
kmc -k28 file2.fastq kmers2 tmp
kmc_tools intersect kmers1 -ci10 -cx200 kmers2 -ci4 -cx100 kmers1_kmers2_intersect -ci20 -cx150

see how each input gets its own little filter squad? kmers1 gets -ci10 -cx200, kmers2 gets -ci4 -cx100, and then the output kmers1_kmers2_intersect gets -ci20 -cx150. main character energy for every single one 💅✨

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👑 AUTHOR 👑

KMC was originally written by:

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

absolute legends, fr fr 🫶

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💖 COPYING 💖

KMC is a free software distributed under GNU GPL3 licence for academic, research, and commercial use. free software, free vibes, iconic behavior no cap 🌈

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okay that's the whole page bestie, go intersect some k-mers, you got this 💅✨

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and that's a wrap on KMC_TOOLS-INTERSECT(1), page header KMC_TOOLS-INTERSECT(1) and footer KMC_TOOLS-INTERSECT(1) alike — same name up top, same name at the bottom, symmetrical queen 💖 mwah, bye!! 🎀🦋