kmers.cpp (1.16 kB)
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Fast kmer counting table algorithm using perfect hash function: C++ pseudo-code integration into R using Rcpp API

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posted on 2016-06-13, 06:45 authored by Macherki M. E.Macherki M. E.
Counting kmers (substrings of length k in DNA sequence data) is an essential component of many methods in bioinformatics, including data preprocessing for de novo assembly, repeat detection, and sequencing coverage estimation. We proposed a simple algorithm to calculate the kmer count using perfect hash table implemented in C++ and using Rcpp API to be able exported into R.