Current sequencing methods produce large amounts of data, but genome assemblies based
on these data are often woefully incomplete. These incomplete and error-filled assemblies …

Assembly of metagenomic sequence data into microbial genomes is of fundamental value to
improving our understanding of microbial ecology and metabolism by elucidating the …

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 …

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 …

High-throughput DNA sequencing technologies have revolutionized genomic analysis,
including the de novo assembly of whole genomes. Nevertheless, assembly of complex …

Aligning sequencing reads onto a reference is an essential step of the majority of genomic
analysis pipelines. Computational algorithms for read alignment have evolved in …

Next-generation sequencing (NGS) approaches rapidly produce millions to billions of short
reads, which allow pathogen detection and discovery in human clinical, animal and …

In computational biology and other sciences, researchers are frequently faced with a choice
between several computational methods for performing data analyses. Benchmarking …

High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid
genomes, and metagenomes provide important insights into genetic variation associated …

Introduction Sex chromosomes originate from ordinary autosomes. Ancient sex-specific W or
Y chromosomes, like that of female chicken or those of male mammals, usually have lost …