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Gerbil: A Fast and Memory-Efficient k-mer Counter with GPU-Support
[article]
2016
arXiv
pre-print
A basic task in bioinformatics is the counting of k-mers in genome strings. The k-mer counting problem is to build a histogram of all substrings of length k in a given genome sequence. We present the open source k-mer counting software Gerbil that has been designed for the efficient counting of k-mers for k≥32. Given the technology trend towards long reads of next-generation sequencers, support for large k becomes increasingly important. While existing k-mer counting tools suffer from excessive
arXiv:1607.06618v1
fatcat:3xvtaxvuqrhizfazrhhfcd6ssi