Alignment-free sequence analyses have been applied to problems ranging from whole-
genome phylogeny to the classification of protein families, identification of horizontally …

Genome sequencing and analysis allow researchers to decode the functional information
hidden in DNA sequences as well as to study cell to cell variation within a cell population …

Typical genotyping workflows map reads to a reference genome before identifying genetic
variants. Generating such alignments introduces reference biases and comes with …

Chardonnay is the basis of some of the world's most iconic wines and its success is
underpinned by a historic program of clonal selection. There are numerous clones of …

Single nucleotide polymorphisms (SNPs) in metagenomics are used to quantify population
structure, track strains and identify genetic determinants of microbial phenotypes. However …

Motivation Selecting a subset of k-mers in a string in a local manner is a common task in
bioinformatics tools for speeding up computation. Arguably the most well-known and …

Detecting genetic variants in metagenomic data is a priority for understanding the evolution,
ecology, and functional characteristics of microbial communities. Many tools that perform this …

Motivation Many bioinformatics algorithms are designed for the analysis of sequences of
some uniform length, conventionally referred to as k-mers. These include de Bruijn graph …

Abstract de Bruijn graphs play an essential role in bioinformatics, yet they lack a universal
scalable representation. Here, we introduce simplitigs as a compact, efficient, and scalable …

We introduce ak-mer-based computational protocol, DE-kupl, for capturing local RNA
variation in a set of RNA-seq libraries, independently of a reference genome or …