Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture

Structural and functional analysis of the finished genome of the recently isolated toxic Anabaena sp. WA102

(2016) Nathan M. Brown et al.   BMC GENOMICS

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Improved metagenome assemblies and taxonomic binning using long-read circular consensus sequence data

(2016) J. A. Frank et al.   Scientific Reports

Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing

(2015) Doori Park et al.   BMC GENOMICS

One chromosome, one contig: complete microbial genomes from long-read sequencing and assembly

(2015) Sergey Koren et al.   CURRENT OPINION IN MICROBIOLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

International Code of Nomenclature of Prokaryotes

(2015) Charles T Parker et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

N2-fixation, ammonium release and N-transfer to the microbial and classical food web within a plankton community

(2015) Birgit Adam et al.   ISME Journal

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning

(2015) Brian Cleary et al.   NATURE BIOTECHNOLOGY

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics

(2015) P. N. Evans et al.   SCIENCE

Stepwise evolution of pandrug-resistance in Klebsiella pneumoniae

(2015) Hosam M. Zowawi et al.   Scientific Reports

Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy

(2015) Masaki Shintani et al.   Frontiers in Microbiology

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics

(2015) Alejandra Escobar-Zepeda et al.   Frontiers in Genetics

Structural Diversity of Bacterial Communities Associated with Bloom-Forming Freshwater Cyanobacteria Differs According to the Cyanobacterial Genus

(2015) Imen Louati et al.   PLoS One

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

Host-Specificity and Dynamics in Bacterial Communities Associated with Bloom-Forming Freshwater Phytoplankton

(2014) Inessa Lacativa Bagatini et al.   PLoS One

The Complete Genome Sequence of Escherichia coli EC958: A High Quality Reference Sequence for the Globally Disseminated Multidrug Resistant E. coli O25b:H4-ST131 Clone

(2014) Brian M. Forde et al.   PLoS One

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Recently publishedStreptomycesgenome sequences

(2014) James Harrison et al.   Microbial Biotechnology

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Reducing assembly complexity of microbial genomes with single-molecule sequencing

(2013) Sergey Koren et al.   GENOME BIOLOGY

REAPR: a universal tool for genome assembly evaluation

(2013) Martin Hunt et al.   GENOME BIOLOGY

Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform

(2013) Erin B Fichot et al.   Microbiome

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

(2012) Elmar Pruesse et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

The Black Queen Hypothesis: Evolution of Dependencies through Adaptive Gene Loss

(2012) J. J. Morris et al.   mBio

RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data

(2011) Y. Zhao et al.   BIOINFORMATICS

A Guide to the Natural History of Freshwater Lake Bacteria

(2011) R. J. Newton et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

Microbial Metagenomics: Beyond the Genome

(2010) Jack A. Gilbert et al.   Annual Review of Marine Science

Motility and Chemotaxis inCampylobacterandHelicobacter

(2010) Paphavee Lertsethtakarn et al.   Annual Review of Microbiology

Carbon and nitrogen fluxes associated with the cyanobacterium Aphanizomenon sp. in the Baltic Sea

(2010) Helle Ploug et al.   ISME Journal

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

A small population of planktonicFlavobacteriawith disproportionally high growth during the spring phytoplankton bloom in a prealpine lake

(2009) Michael Zeder et al.   ENVIRONMENTAL MICROBIOLOGY

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

High diversity of cultivable heterotrophic bacteria in association with cyanobacterial water blooms

(2008) Katri A Berg et al.   ISME Journal

The minimum information about a genome sequence (MIGS) specification

(2008) Dawn Field et al.   NATURE BIOTECHNOLOGY