Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics

An evaluation of the accuracy and speed of metagenome analysis tools

(2016) Stinus Lindgreen et al.   Scientific Reports

Spaced seeds improvek-mer-based metagenomic classification

(2015) Karel Břinda et al.   BIOINFORMATICS

NoDe: a fast error-correction algorithm for pyrosequencing amplicon reads

(2015) Mohamed Mysara et al.   BMC BIOINFORMATICS

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

(2015) Rachid Ounit et al.   BMC GENOMICS

Microbial Community Composition and Diversity via 16S rRNA Gene Amplicons: Evaluating the Illumina Platform

(2015) Lucas Sinclair et al.   PLoS One

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

(2015) Sarah L. Westcott et al.   PeerJ

The ocean sampling day consortium

(2015) Anna Kopf et al.   GigaScience

Consistency of metagenomic assignment programs in simulated and real data

(2014) Koldo Garcia-Etxebarria et al.   BMC BIOINFORMATICS

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data

(2014) Ségolène Caboche et al.   BMC GENOMICS

How many16S-based studies should be included in a metagenomic conference? It may be a matter of etymology

(2014) Alfonso Esposito et al.   FEMS MICROBIOLOGY LETTERS

Microbiota characterization of a Belgian protected designation of origin cheese, Herve cheese, using metagenomic analysis

(2014) V. Delcenserie et al.   JOURNAL OF DAIRY SCIENCE

Data analysis for 16S microbial profiling from different benchtop sequencing platforms

(2014) Victor S. Pylro et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Comparative Metagenomic Analysis of Human Gut Microbiome Composition Using Two Different Bioinformatic Pipelines

(2014) Valeria D’Argenio et al.   Biomed Research International

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Swarm: robust and fast clustering method for amplicon-based studies

(2014) Frédéric Mahé et al.   PeerJ

Design and Experimental Application of a Novel Non-Degenerate Universal Primer Set that Amplifies Prokaryotic 16S rRNA Genes with a Low Possibility to Amplify Eukaryotic rRNA Genes

(2013) H. Mori et al.   DNA RESEARCH

Computational meta'omics for microbial community studies

(2013) N. Segata et al.   Molecular Systems Biology

Surprisingly extensive mixed phylogenetic and ecological signals among bacterial Operational Taxonomic Units

(2013) Alexander F. Koeppel et al.   NUCLEIC ACIDS RESEARCH

Assessing the Consequences of Denoising Marker-Based Metagenomic Data

(2013) John M. Gaspar et al.   PLoS One

Assessing the Fecal Microbiota: An Optimized Ion Torrent 16S rRNA Gene-Based Analysis Protocol

(2013) Christian Milani et al.   PLoS One

Comparing clustering and pre-processing in taxonomy analysis

(2012) Marc J. Bonder et al.   BIOINFORMATICS

A comparative evaluation of sequence classification programs

(2012) Adam L Bazinet et al.   BMC BIOINFORMATICS

Coverage evaluation of universal bacterial primers using the metagenomic datasets

(2012) Dan-Ping Mao et al.   BMC MICROBIOLOGY

Fast, accurate error-correction of amplicon pyrosequences using Acacia

(2012) Lauren Bragg et al.   NATURE METHODS

Grinder: a versatile amplicon and shotgun sequence simulator

(2012) Florent E. Angly et al.   NUCLEIC ACIDS RESEARCH

Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities

(2012) John Martin et al.   PLoS One

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Evaluation of short read metagenomic assembly

(2011) Anveshi Charuvaka et al.   BMC GENOMICS

Evaluating the Fidelity of De Novo Short Read Metagenomic Assembly Using Simulated Data

(2011) Miguel Pignatelli et al.   PLoS One

Metagenomic Analyses: Past and Future Trends

(2010) Carola Simon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Short clones or long clones? A simulation study on the use of paired reads in metagenomics

(2010) Suparna Mitra et al.   BMC BIOINFORMATICS

V-Xtractor: An open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences

(2010) Martin Hartmann et al.   JOURNAL OF MICROBIOLOGICAL METHODS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY