Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

(2018) Robert D. Stewart et al.   Nature Communications

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Asgard archaea illuminate the origin of eukaryotic cellular complexity

(2017) Katarzyna Zaremba-Niedzwiedzka et al.   NATURE

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI)

(2017) Chongyi Chen et al.   SCIENCE

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes

(2016) Karin Troell et al.   BMC GENOMICS

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Strategies to improve reference databases for soil microbiomes

(2016) Jinlyung Choi et al.   ISME Journal

Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria

(2016) Alexander Eiler et al.   ISME Journal

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates

(2016) Kaston Leung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved Environmental Genomes via Integration of Metagenomic and Single-Cell Assemblies

(2016) Daniel R. Mende et al.   Frontiers in Microbiology

Recovering complete and draft population genomes from metagenome datasets

(2016) Naseer Sangwan et al.   Microbiome

Single-Cell-Genomics-Facilitated Read Binning of Candidate Phylum EM19 Genomes from Geothermal Spring Metagenomes

(2015) Eric D. Becraft et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling

(2015) Markus V. Lindh et al.   ENVIRONMENTAL MICROBIOLOGY

Phylogeny and physiology of candidate phylum ‘Atribacteria’ (OP9/JS1) inferred from cultivation-independent genomics

(2015) Masaru K Nobu et al.   ISME Journal

Complex archaea that bridge the gap between prokaryotes and eukaryotes

(2015) Anja Spang et al.   NATURE

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Structure and function of the global ocean microbiome

(2015) S. Sunagawa et al.   SCIENCE

Classifying the uncultivated microbial majority: A place for metagenomic data in the Candidatus proposal

(2015) Konstantinos T. Konstantinidis et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

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

(2015) Dongwan D. Kang et al.   PeerJ

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Comparative single-cell genomics reveals potential ecological niches for the freshwater acI Actinobacteria lineage

(2014) Trevor W Ghylin et al.   ISME Journal

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Obtaining genomes from uncultivated environmental microorganisms using FACS–based single-cell genomics

(2014) Christian Rinke et al.   Nature Protocols

Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition

(2014) Chris L. Dupont et al.   PLoS One

Cryptic carbon and sulfur cycling between surface ocean plankton

(2014) Bryndan P. Durham et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus

(2014) N. Kashtan et al.   SCIENCE

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

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

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

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

UGA is an additional glycine codon in uncultured SR1 bacteria from the human microbiota

(2013) J. H. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Elmar Pruesse et al.   BIOINFORMATICS

Single cell genomics: an individual look at microbes

(2012) Ramunas Stepanauskas   CURRENT OPINION IN MICROBIOLOGY

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

Metagenome, metatranscriptome and single-cell sequencing reveal microbial response to Deepwater Horizon oil spill

(2012) Olivia U Mason et al.   ISME Journal

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

Classification and clustering of sequencing data using a Poisson model

(2011) Daniela M. Witten   Annals of Applied Statistics

WebMGA: a customizable web server for fast metagenomic sequence analysis

(2011) Sitao Wu et al.   BMC GENOMICS

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea

(2011) Daniel PR Herlemann et al.   ISME Journal

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Decontamination of MDA Reagents for Single Cell Whole Genome Amplification

(2011) Tanja Woyke et al.   PLoS One

Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

(2011) B. K. Swan et al.   SCIENCE

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Global patterns in the biogeography of bacterial taxa

(2010) Diana R. Nemergut et al.   ENVIRONMENTAL MICROBIOLOGY

One Bacterial Cell, One Complete Genome

(2010) Tanja Woyke et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Pyrosequencing reveals contrasting seasonal dynamics of taxa within Baltic Sea bacterioplankton communities

(2009) Anders F Andersson et al.   ISME Journal

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

(2009) Dongying Wu et al.   NATURE

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Community-wide analysis of microbial genome sequence signatures

(2009) Gregory J Dick et al.   GENOME BIOLOGY

The Microbial Engines That Drive Earth's Biogeochemical Cycles

(2008) P. G. Falkowski et al.   SCIENCE