Microbiome research has grown rapidly over the past decade, with a proliferation of new
methods that seek to make sense of large, complex data sets. Here, we survey two of the …

The study of metagenomics has been much benefited from low-cost and high-throughput
sequencing technologies, yet the tremendous amount of data generated make analysis like …

While metagenomics has emerged as a technology of choice for analyzing bacterial
populations, the assembly of metagenomic data remains challenging, thus stifling biological …

The assembly of DNA sequences de novo is fundamental to genomics research. It is the first
of many steps toward elucidating and characterizing whole genomes. Downstream …

MEGAHIT is a NGS de novo assembler for assembling large and complex metagenomics
data in a time-and cost-efficient manner. It finished assembling a soil metagenomics dataset …

Low-cost whole-genome assembly has enabled the collection of haplotype-resolved
pangenomes for numerous organisms. In turn, this technological change is encouraging the …

Metagenomics is a segment of conventional microbial genomics dedicated to the
sequencing and analysis of combined genomic DNA of entire environmental samples. The …

Abstract Background The de Bruijn graph data structure is widely used in next-generation
sequencing (NGS). Many programs, eg de novo assemblers, rely on in-memory …

We propose a generic approach to replace the canonical sequence representation of
genomes with graph representations, and study several applications of such extensions. We …

The microbiome can be defined as the community of microorganisms that live in a particular
environment. Metagenomics is the practice of sequencing DNA from the genomes of all …