Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences

(2017) Imchang Lee et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

(2017)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Application of next generation sequencing in clinical microbiology and infection prevention

(2017) Ruud H. Deurenberg et al.   JOURNAL OF BIOTECHNOLOGY

bcgTree: automatized phylogenetic tree building from bacterial core genomes

(2016) Markus J. Ankenbrand et al.   GENOME

OrthoANI: An improved algorithm and software for calculating average nucleotide identity

(2016) Imchang Lee et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa

(2016) Vartul Sangal et al.   Scientific Reports

Genome-Based Taxonomic Classification of Bacteroidetes

(2016) Richard L. Hahnke et al.   Frontiers in Microbiology

JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison

(2015) Michael Richter et al.   BIOINFORMATICS

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

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

Multilocus sequence analysis (MLSA) in prokaryotic taxonomy

(2015) Stefanie P. Glaeser et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Past and future species definitions for Bacteria and Archaea

(2015) Ramon Rosselló-Móra et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Completing bacterial genome assemblies: strategy and performance comparisons

(2015) Yu-Chieh Liao et al.   Scientific Reports

Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea

(2014) J. Chun et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes

(2014) M. Kim et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Bioinformatic Genome Comparisons for Taxonomic and Phylogenetic Assignments Using Aeromonas as a Test Case

(2014) Sophie M. Colston et al.   mBio

Genome sequence-based species delimitation with confidence intervals and improved distance functions

(2013) Jan P Meier-Kolthoff et al.   BMC BIOINFORMATICS

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

BIGSdb: Scalable analysis of bacterial genome variation at the population level

(2011) Keith A Jolley et al.   BMC BIOINFORMATICS

Genomic taxonomy of vibrios

(2009) Cristiane C Thompson et al.   BMC EVOLUTIONARY BIOLOGY

Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae

(2009) J. Chun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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