Since the early days of the genome era, the scientific community has relied on a single
'reference'genome for each species, which is used as the basis for a wide range of genetic …

High-throughput sequencing data sets are usually deposited in public repositories (eg, the
European Nucleotide Archive) to ensure reproducibility. As the amount of data has reached …

Memory consumption of de Bruijn graphs is often prohibitive. Most de Bruijn graph-based
assemblers reduce the complexity by compacting paths into single vertices, but this is …

Exponentially increasing amounts of unprocessed bacterial and viral genomic sequence
data are stored in the global archives. The ability to query these data for sequence search …

Motivation Huge datasets containing whole-genome sequences of bacterial strains are now
commonplace and represent a rich and important resource for modern genomic …

Background In nature, microbial communities undergo changes in composition that threaten
their resiliency. Here, we interrogated sourdough, a natural cereal-fermenting …

Microbial genome-wide association studies (mGWAS) are a new and exciting research field
that is adapting human GWAS methods to understand how variations in microbial genomes …

Sequence-level searches on large collections of RNA sequencing experiments, such as the
NCBI Sequence Read Archive (SRA), would enable one to ask many questions about the …

Reliable detection of somatic variations is of critical importance in cancer research. Here we
present Lancet, an accurate and sensitive somatic variant caller, which detects SNVs and …

We present COBS, a COmpact Bit-sliced Signature index, which is a cross-over between an
inverted index and Bloom filters. Our target application is to index k-mers of DNA samples or …