Synthetic microbe communities provide internal reference standards for metagenome sequencing and analysis

RLE plots: Visualizing unwanted variation in high dimensional data

(2018) Luke C. Gandolfo et al.   PLoS One

Shotgun metagenomics, from sampling to analysis

(2017) Christopher Quince et al.   NATURE BIOTECHNOLOGY

Reference standards for next-generation sequencing

(2017) Simon A. Hardwick et al.   NATURE REVIEWS GENETICS

Statistical evaluation of methods for identification of differentially abundant genes in comparative metagenomics

(2016) Viktor Jonsson et al.   BMC GENOMICS

Toward Accurate and Quantitative Comparative Metagenomics

(2016) Stephen Nayfach et al.   CELL

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

High-resolution phylogenetic microbial community profiling

(2016) Esther Singer et al.   ISME Journal

Assuring the Quality of Next-Generation Sequencing in Clinical Microbiology and Public Health Laboratories

(2016) Amy S. Gargis et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Plasmid-Based Materials as Multiplex Quality Controls and Calibrators for Clinical Next-Generation Sequencing Assays

(2016) David J. Sims et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Representing genetic variation with synthetic DNA standards

(2016) Ira W Deveson et al.   NATURE METHODS

Spliced synthetic genes as internal controls in RNA sequencing experiments

(2016) Simon A Hardwick et al.   NATURE METHODS

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

(2016) Ivan Sović et al.   Nature Communications

Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples

(2016) Angela Glassing et al.   Gut Pathogens

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

(2016) Christian Rinke et al.   PeerJ

Adjusting microbiome profiles for differences in microbial load by spike-in bacteria

(2016) Frank Stämmler et al.   Microbiome

Next generation sequencing data of a defined microbial mock community

(2016) Esther Singer et al.   Scientific Data

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

MetaQUAST: evaluation of metagenome assemblies

(2015) Alla Mikheenko et al.   BIOINFORMATICS

Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community

(2015) Robert M. Bowers et al.   BMC GENOMICS

Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities

(2015) Jacob Moran-Gilad et al.   BMC INFECTIOUS DISEASES

Microbial diversity—exploration of natural ecosystems and microbiomes

(2015) Sean M Gibbons et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A complete bacterial genome assembled de novo using only nanopore sequencing data

(2015) Nicholas J Loman et al.   NATURE METHODS

Improved data analysis for the MinION nanopore sequencer

(2015) Miten Jain et al.   NATURE METHODS

Library preparation methodology can influence genomic and functional predictions in human microbiome research

(2015) Marcus B. Jones et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Making the Leap from Research Laboratory to Clinic: Challenges and Opportunities for Next-Generation Sequencing in Infectious Disease Diagnostics

(2015) Brittany Goldberg et al.   mBio

Poretools: a toolkit for analyzing nanopore sequence data

(2014) N. J. Loman et al.   BIOINFORMATICS

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

Update on RefSeq microbial genomes resources

(2014) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures

(2014) Sarah A. Munro et al.   Nature Communications

Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly

(2013) Yen-Chun Chen et al.   PLoS One

Revisiting Global Gene Expression Analysis

(2012) Jakob Lovén et al.   CELL

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research

(2012)   PLoS One

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

ART: a next-generation sequencing read simulator

(2011) Weichun Huang et al.   BIOINFORMATICS

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

Individual genome assembly from complex community short-read metagenomic datasets

(2011) Chengwei Luo et al.   ISME Journal

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Evaluation of time profile reconstruction from complex two-color microarray designs

(2008) Ana C Fierro et al.   BMC BIOINFORMATICS