… I/O parallelism we propose a very competitive k-mer counting procedure, called KMC. Our
… least some bioinformatics problems with massive data on a commodity personal computer. …

… with a low false positive of 1%, the memory usage is competitive with Tallymer and
Jellyfish; with a higher 5% false positive rate, the memory usage is lower than all but the disk-based …

… k-mer counting, on large datasets about twice faster than the strongest competitors (Jellyfish
2, KMC 1), using about 12 GB (or less) of RAM. Our disk-based … PC with an solid-state disk. …

… popular k-mer counters, but we also cover experimental analysis of k-mer counting tools to
… The disk-based approach to k-mer counting has a much lower memory requirement than in-…

… k-mers by filtering out singleton k-mers [5], and the development of disk-based algorithms
to … Grabowski, “Disk-based kmer counting on a PC,” BMC Bioinformatics, vol. 14, no. 1, p. …

… For many genomics applications, such as K-mer counting, the off-chip DRAM (and sometimes
… In this paper we describe how and why K-mer counting is one such use for an FPGA-…

… An example of a disk based counter is DSK [13] and can run with a very low amount of RAM…
they come back from the FPGAs to the PC since some FPGAs may return results faster than …

… -fast k-mer counting algorithm, KCOSS, to fulfill k-mer counting … Disk-based k-mer counting
algorithm deploys disk as the … Usually, disk-based k-mer counters (Audano and Vannberg, …

… BFCounter [6] uses bloom filters for k-mer counting to filter out rarely occurring k-mers …
concept of minimizers to the k-mer counting, thus further optimizing the disk-based approach. The …

… storage of k-mer sets, eg for de Bruijn graphs or alignment indexes. Here, we introduce the
K-mer File Format as a general lossless framework for storing and manipulating k-mer sets, …