Scalable metagenomic taxonomy classification using a reference genome database

Taxonomic binning of metagenome samples generated by next-generation sequencing technologies

(2012) J. Droge et al.   BRIEFINGS IN BIOINFORMATICS

Classification of metagenomic sequences: methods and challenges

(2012) S. S. Mande et al.   BRIEFINGS IN BIOINFORMATICS

Current opportunities and challenges in microbial metagenome analysis--a bioinformatic perspective

(2012) H. Teeling et al.   BRIEFINGS IN BIOINFORMATICS

Compressive genomics

(2012) Po-Ru Loh et al.   NATURE BIOTECHNOLOGY

Unlocking the potential of metagenomics through replicated experimental design

(2012) Rob Knight et al.   NATURE BIOTECHNOLOGY

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

(2012) Daniel R. Mende et al.   PLoS One

Fast and Accurate Taxonomic Assignments of Metagenomic Sequences Using MetaBin

(2012) Vineet K. Sharma et al.   PLoS One

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

(2012) John Martin et al.   PLoS One

Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads

(2012) Colin F. Davenport et al.   PLoS One

Scaling metagenome sequence assembly with probabilistic de Bruijn graphs

(2012) J. Pell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing

(2012) Andreas Keller et al.   Nature Communications

A robust and accurate binning algorithm for metagenomic sequences with arbitrary species abundance ratio

(2011) H. C. M. Leung et al.   BIOINFORMATICS

Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences

(2011) Bo Liu et al.   BMC GENOMICS

PhymmBL expanded: confidence scores, custom databases, parallelization and more

(2011) Arthur Brady et al.   NATURE METHODS

Plantagora: Modeling Whole Genome Sequencing and Assembly of Plant Genomes

(2011) Roger Barthelson et al.   PLoS One

Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing

(2011) Samuel V. Angiuoli et al.   PLoS One

SPHINX—an algorithm for taxonomic binning of metagenomic sequences

(2010) Monzoorul Haque Mohammed et al.   BIOINFORMATICS

Cloud computing and the DNA data race

(2010) Michael C Schatz et al.   NATURE BIOTECHNOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

(2008) Daniel C. Richter et al.   PLoS One