The khmer package is a freely available software library for working efficiently with fixed
length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer …

Background De novo transcriptome assemblies are required prior to analyzing RNA
sequencing data from a species without an existing reference genome or transcriptome …

Microbial communities in marine oxygen deficient zones (ODZs) are responsible for up to
half of marine N loss through conversion of nutrients to N2O and N2. This N loss is …

Motivation Third-generation sequencing technologies can sequence long reads that contain
as many as 2 million base pairs. These long reads are used to construct an assembly (ie the …

We evaluate the performance of three metagenome assemblers, IDBA, MetaSPAdes, and
MEGAHIT, on short-read sequencing of a defined “mock” community containing 64 genomes …

Since their emergence around 2006, Next-Generation Sequencing technologies have been
revolutionizing biological and medical research. Obtaining instantly an extensive amount of …

Abstract Motivation De Bruijn graphs are a common assembly data structure for sequencing
datasets. But with the advances in sequencing technologies, assembling high coverage …

Genomes computationally inferred from large metagenomic data sets are often incomplete
and may be missing functionally important content and strain variation. We introduce an …

Background Specialized data structures are required for online algorithms to efficiently
handle large sequencing datasets. The counting quotient filter (CQF), a compact hashtable …

Comparative analysis of Clostridioides difficile whole-genome sequencing (WGS) data
enables fine scaled investigation of transmission and is increasingly becoming part of …