Accurate and complete genomes from metagenomes

Basic local alignment search tool

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The Sequence Alignment/Map format and SAMtools

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Fast gapped-read alignment with Bowtie 2

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IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

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Integrative genomics viewer

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CheckM: Assessing the Quality of Microbial Genomes Recovered from Isolates, Single Cells, and Metagenomes

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Prodigal: prokaryotic gene recognition and translation initiation site identification

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trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

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A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

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Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

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Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

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Accelerated Profile HMM Searches

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The human microbiome project

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metaSPAdes: a new versatile metagenomic assembler

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The COG database: a tool for genome-scale analysis of protein functions and evolution

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Capturing Chromosome Conformation

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A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

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

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A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach

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Snakemake—a scalable bioinformatics workflow engine

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Complete nitrification by Nitrospira bacteria

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Binning metagenomic contigs by coverage and composition

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tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

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MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

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

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Community structure and metabolism through reconstruction of microbial genomes from the environment

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Insights into the phylogeny and coding potential of microbial dark matter

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A new view of the tree of life

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

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Complete nitrification by a single microorganism

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

Parks, D. H., Rinke, C., Chuvochina, M., Chaumeil, P.-A., Woodcroft, B. J., Evans, P. N., Hugenholtz, P., & Tyson, G. W. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0012-7 · Cited by 1,882 · see citing works

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

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Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

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Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

Pasolli, E., Asnicar, F., Manara, S., Zolfo, M., Karcher, N., Armanini, F., Beghini, F., Manghi, P., Tett, A., Ghensi, P., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.001 · Cited by 1,591 · see citing works

Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS

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A new genomic blueprint of the human gut microbiota

Almeida, A., Mitchell, A. L., Boland, M., Forster, S. C., Gloor, G. B., Tarkowska, A., Lawley, T. D., & Finn, R. D. (2019) · Nature · doi:10.1038/s41586-019-0965-1 · Cited by 1,314 · see citing works

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

Albertsen, M., Hugenholtz, P., Skarshewski, A., Nielsen, K. L., Tyson, G. W., & Nielsen, P. H. (2013) · Nature Biotechnology · doi:10.1038/nbt.2579 · Cited by 1,253 · see citing works

Unusual biology across a group comprising more than 15% of domain Bacteria

Brown, C. T., Hug, L. A., Thomas, B. C., Sharon, I., Castelle, C. J., Singh, A., Wilkins, M. J., Wrighton, K. C., Williams, K. H., & Banfield, J. F. (2015) · Nature · doi:10.1038/nature14486 · Cited by 1,216 · see citing works

VirSorter: mining viral signal from microbial genomic data

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Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system

Anantharaman, K., Brown, C., Hug, L., Sharon, I., Castelle, C., Probst, A., Thomas, B., Singh, A., Wilkins, M., Karaoz, U., et al. (2016) · Nature Communications · doi:10.1038/ncomms13219 · Cited by 1,040 · see citing works

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea

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New insights from uncultivated genomes of the global human gut microbiome

Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S., & Kyrpides, N. C. (2019) · Nature · doi:10.1038/s41586-019-1058-x · Cited by 737 · see citing works

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm

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From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy

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hybrid SPA des : an algorithm for hybrid assembly of short and long reads

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Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla

Wrighton, K. C., Thomas, B. C., Sharon, I., Miller, C. S., Castelle, C. J., VerBerkmoes, N. C., Wilkins, M. J., Hettich, R. L., Lipton, M. S. W., Williams, K. H., et al. (2012) · Science · doi:10.1126/science.1224041 · Cited by 643 · see citing works

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

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High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

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Assessing the performance of the Oxford Nanopore Technologies MinION

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Potential for Chemolithoautotrophy Among Ubiquitous Bacteria Lineages in the Dark Ocean

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Complete Genome Sequence of Citrus Huanglongbing Bacterium, ‘CandidatusLiberibacter asiaticus’ Obtained Through Metagenomics

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Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle

He, X., McLean, J. S., Edlund, A., Yooseph, S., Hall, A. P., Liu, S.-Y., Dorrestein, P. C., Esquenazi, E., Hunter, R. C., Cheng, G., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1419038112 · Cited by 549 · see citing works

SAR11 Bacteria: The Most Abundant Plankton in the Oceans

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Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling

Castelle, C. J., Wrighton, K. C., Thomas, B. C., Hug, L. A., Brown, C. T., Wilkins, M. J., Frischkorn, K. R., Tringe, S. G., Singh, A., Markillie, L. M., et al. (2015) · Current Biology · doi:10.1016/j.cub.2015.01.014 · Cited by 536 · see citing works

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

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Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth

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The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans

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Clades of huge phages from across Earth’s ecosystems

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

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Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

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Diverse uncultivated ultra-small bacterial cells in groundwater

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VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

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Analyzing genomes with cumulative skew diagrams

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Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

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Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle

Anantharaman, K., Hausmann, B., Jungbluth, S. P., Kantor, R. S., Lavy, A., Warren, L. A., Rappé, M. S., Pester, M., Loy, A., Thomas, B. C., et al. (2018) · The ISME Journal · doi:10.1038/s41396-018-0078-0 · Cited by 432 · see citing works

The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria

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Measurement of bacterial replication rates in microbial communities

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Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data

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GapFiller: a de novo assembly approach to fill the gap within paired reads

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“ Candidatus Cloacamonas Acidaminovorans”: Genome Sequence Reconstruction Provides a First Glimpse of a New Bacterial Division

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Complete Genome Structure of the Thermophilic Cyanobacterium Thermosynechococcus elongatus BP-1

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Enigmatic, ultrasmall, uncultivated Archaea

Baker, B. J., Comolli, L. R., Dick, G. J., Hauser, L., Hyatt, D., Dill, B. D., Land, M., VerBerkmoes, N. C., Hettich, R. L., & Banfield, J. F. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0914470107 · Cited by 348 · see citing works

Oligotyping analysis of the human oral microbiome

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Geospatial Resolution of Human and Bacterial Diversity with City-Scale Metagenomics

Afshinnekoo, E., Meydan, C., Chowdhury, S., Jaroudi, D., Boyer, C., Bernstein, N., Maritz, J. M., Reeves, D., Gandara, J. A., Chhangawala, S., et al. (2015) · Cell Systems · doi:10.1016/j.cels.2015.01.001 · Cited by 331 · see citing works

Evidence for symmetric chromosomal inversions around the replication origin in bacteria

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Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla

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The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle

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The blood DNA virome in 8,000 humans

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Ultra-deep, long-read nanopore sequencing of mock microbial community standards

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

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Linking the resistome and plasmidome to the microbiome

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DNA Replication in the Archaea

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Single-cell genomics

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Genome-reconstruction for eukaryotes from complex natural microbial communitiesPreprint

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Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface

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Single cell genomics: an individual look at microbes

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