The most frequently used sequencing technologies and assembly methods in different time segments of the bacterial surveillance and RefSeq genome databases
B Segerman - Frontiers in cellular and infection microbiology, 2020 - frontiersin.org
Whole genome sequencing has become a powerful tool in modern microbiology. Especially
bacterial genomes are sequenced in high numbers. Whole genome sequencing is not only …
bacterial genomes are sequenced in high numbers. Whole genome sequencing is not only …
SKESA: strategic k-mer extension for scrupulous assemblies
A Souvorov, R Agarwala, DJ Lipman - Genome biology, 2018 - Springer
SKESA is a DeBruijn graph-based de-novo assembler designed for assembling reads of
microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit …
microbial genomes sequenced using Illumina. Comparison with SPAdes and MegaHit …
Mutant phenotypes for thousands of bacterial genes of unknown function
MN Price, KM Wetmore, RJ Waters, M Callaghan… - Nature, 2018 - nature.com
One-third of all protein-coding genes from bacterial genomes cannot be annotated with a
function. Here, to investigate the functions of these genes, we present genome-wide mutant …
function. Here, to investigate the functions of these genes, we present genome-wide mutant …
Functional overlap of the Arabidopsis leaf and root microbiota
Roots and leaves of healthy plants host taxonomically structured bacterial assemblies, and
members of these communities contribute to plant growth and health. We established …
members of these communities contribute to plant growth and health. We established …
Modular traits of the Rhizobiales root microbiota and their evolutionary relationship with symbiotic rhizobia
Rhizobia are a paraphyletic group of soil-borne bacteria that induce nodule organogenesis
in legume roots and fix atmospheric nitrogen for plant growth. In non-leguminous plants …
in legume roots and fix atmospheric nitrogen for plant growth. In non-leguminous plants …
A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data
Motivation: Open-source bacterial genome assembly remains inaccessible to many
biologists because of its complexity. Few software solutions exist that are capable of …
biologists because of its complexity. Few software solutions exist that are capable of …
Assembling single-cell genomes and mini-metagenomes from chimeric MDA products
Recent advances in single-cell genomics provide an alternative to largely gene-centric
metagenomics studies, enabling whole-genome sequencing of uncultivated bacteria …
metagenomics studies, enabling whole-genome sequencing of uncultivated bacteria …
Assembling genomes and mini-metagenomes from highly chimeric reads
Recent advances in single-cell genomics provide an alternative to gene-centric
metagenomics studies, enabling whole genome sequencing of uncultivated bacteria …
metagenomics studies, enabling whole genome sequencing of uncultivated bacteria …
Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota
Roots of different plant species are colonized by bacterial communities, that are distinct even
when hosts share the same habitat. It remains unclear to what extent the host actively …
when hosts share the same habitat. It remains unclear to what extent the host actively …
Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen
Genomic plasticity enables adaptation to changing environments, which is especially
relevant for pathogens that engage in “arms races” with their hosts. In many pathogens …
relevant for pathogens that engage in “arms races” with their hosts. In many pathogens …