Many disciplines, from human genetics and oncology to plant breeding, microbiology and
virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes …

SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of
microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit …

Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and
monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify …

Evaluating metagenomic software is key for optimizing metagenome interpretation and focus
of the Initiative for the Critical Assessment of Metagenome Interpretation (CAMI). The CAMI II …

Characterizing the errors generated by common high-throughput sequencing platforms and
telling true genetic variation from technical artefacts are two interdependent steps, essential …

Genome-wide association study (GWAS) methods applied to bacterial genomes have
shown promising results for genetic marker discovery or detailed assessment of marker …

Motivation: As the quantity of data per sequencing experiment increases, the challenges of
fragment assembly are becoming increasingly computational. The de Bruijn graph is a …

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 …

Background Microbial inhabitants of soils are important to ecosystem and planetary
functions, yet there are large gaps in our knowledge of their diversity and ecology. The …

BFC is a free, fast and easy-to-use sequencing error corrector designed for Illumina short
reads. It uses a non-greedy algorithm but still maintains a speed comparable to …