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

refresh-bio / KMC

Fast and frugal disk based k-mer counter

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How to quickly find the position of k-mer on the genome #167

Open slbai01 opened 3 years ago

slbai01 commented 3 years ago

After comparing two genomes to obtain a large number of unique k-mers, 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.

marekkokot commented 3 years ago

Well, it is not really a scope of KMC. KMC just counts k-mers and with KMC tools you may perform some set operations on KMC databases. Positions of k-mers are not kept in KMC database.