Fast and accurate metagenotyping of the human gut microbiome with GT-Pro

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

(2019) Edoardo Pasolli et al.   CELL

Inferring bacterial recombination rates from large-scale sequencing datasets

(2019) Mingzhi Lin et al.   NATURE METHODS

Impact of Homologous Recombination on the Evolution of Prokaryotic Core Genomes

(2019) Pedro González-Torres et al.   mBio

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

(2019) Nandita R. Garud et al.   PLOS BIOLOGY

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

(2019) Yuanqiang Zou et al.   NATURE BIOTECHNOLOGY

Novel insights from uncultivated genomes of the global human gut microbiome

(2019) Stephen Nayfach et al.   NATURE

A new genomic blueprint of the human gut microbiota

(2019) Alexandre Almeida et al.   NATURE

Fast detection of maximal exact matches via fixed sampling of query K-mers and Bloom filtering of index K-mers

(2019) Yuansheng Liu et al.   BIOINFORMATICS

Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism

(2019) Vayu Maini Rekdal et al.   SCIENCE

The Landscape of Genetic Content in the Gut and Oral Human Microbiome

(2019) Braden T. Tierney et al.   Cell Host & Microbe

Population Genetics in the Human Microbiome

(2019) Nandita R. Garud et al.   TRENDS IN GENETICS

Impacts of florfenicol on the microbiota landscape and resistome as revealed by metagenomic analysis

(2019) Qifan Zeng et al.   Microbiome

Simulating Illumina Metagenomic Data with InSilicoSeq

(2018) Hadrien Gourlé et al.   BIOINFORMATICS

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Gut microbiome structure and metabolic activity in inflammatory bowel disease

(2018) Eric A. Franzosa et al.   Nature Microbiology

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania

(2017) Samuel A. Smits et al.   SCIENCE

metaSNV: A tool for metagenomic strain level analysis

(2017) Paul Igor Costea et al.   PLoS One

Fast genotyping of known SNPs through approximatek-mer matching

(2016) Ariya Shajii et al.   BIOINFORMATICS

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

(2016) Stephen Nayfach et al.   GENOME RESEARCH

Bloom and bust: intestinal microbiota dynamics in response to hospital exposures and Clostridium difficile colonization or infection

(2016) Caroline Vincent et al.   Microbiome

CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers

(2015) Rachid Ounit et al.   BMC GENOMICS

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

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

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

ConStrains identifies microbial strains in metagenomic datasets

(2015) Chengwei Luo et al.   NATURE BIOTECHNOLOGY

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Inference of the Properties of the Recombination Process from Whole Bacterial Genomes

(2013) M. Azim Ansari et al.   GENETICS

Accurate and universal delineation of prokaryotic species

(2013) Daniel R Mende et al.   NATURE METHODS

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

(2012) Jens Roat Kultima et al.   PLoS One

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Clostridium difficile Colonization in Early Infancy Is Accompanied by Changes in Intestinal Microbiota Composition

(2010) C. Rousseau et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

High frequency of hotspot mutations in core genes of Escherichia coli due to short-term positive selection

(2009) S. Chattopadhyay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Clostridium difficile and inflammatory bowel disease

(2008) Mazen Issa et al.   INFLAMMATORY BOWEL DISEASES