Question

How to quickly find the position of k-mer on the genome

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3.1 years ago

slbai00001 • 0

Hi, all

How to quickly find the position of k-mers on the genome? Currently, I use software such as bwa and fuzznucl, but I feel it is not fast enough.

alignment sequencing k-mer • 1.6k views

ADD COMMENT • link updated 2.0 years ago by Christophe • 0 • written 3.1 years ago by slbai00001 • 0

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Are you looking to find one specific k-mer or a map of all k-mers?

ADD REPLY • link 3.1 years ago by Malte Petersen ▴ 40

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In fact, I first used kmc to obtain all the specific k-mers of one genome relative to the other genome, and then I wanted to obtain the position of these k-mers on the genome. The number of k-mers was about several million or even a few giga.

ADD REPLY • link 3.1 years ago by slbai00001 • 0

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Yes. Can I ask for your penultimate goal? Unless you're going to write a new assembler, I'm not sure what you would need that map for.

ADD REPLY • link 3.1 years ago by Malte Petersen ▴ 40

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Did you find an efficient solution? I would like to perform the same task.

ADD REPLY • link 2.0 years ago by Christophe • 0

score 0 · Answer 1 · 2021-03-22

Something similar has been asked here. In essence, you can use motif finding tools such as fuzznuc from the EMBOSS suite, BLAT with a small tile size and options -minMatch and -minIdentity, or seqkit locate, depending on your input/output format requirement.

But yes, as you already noticed, it will be slow because there are lots of k-mers. You could also format your k-mer list in fastq/fasta format and use BWA with zero mismatches allowed.