Background Shotgun metagenomics provides powerful insights into microbial community
biodiversity and function. Yet, inferences from metagenomic studies are often limited by …

Genomic datasets are growing dramatically as the cost of sequencing continues to decline
and small sequencing devices become available. Enormous community databases store …

This paper presents the survey of three algorithms to transform atomic-level molecular
snapshots from molecular dynamics (MD) simulations into metadata representations that are …

Counting the abundance of all the distinct kmers in biological sequence data is a
fundamental step in bioinformatics. These applications include de novo genome assembly …

A fundamental step in many bioinformatics computations is to count the frequency of fixed-
length sequences, called k-mers, a problem that has received considerable attention as an …

De novo genome assembly is a fundamental problem in the field of bioinformatics, that aims
to assemble the DNA sequence of an unknown genome from numerous short DNA …

Identification of known genetic traits and disease-related variants within an individual
requires a fundamental task: genotyping a set of variants from a database. However, the …

K-mer counting is a requisite process for DNA assembly because it speeds up its overall
process. The frequency of K-mers is used for estimating the parameters of DNA assembly …

Analyzing large volumes of data is becoming more and more important in various scientific
computing domains. MapReduce over MPI frameworks are an appealing solution to enable …

K-mers form the backbone of many bioinformatic algorithms. They are, however, difficult to
store and use efficiently because the number of k-mers increases exponentially as k …