Short-read reading-frame predictors are not created equal: sequence error causes loss of signal

The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools

(2012) Andreas Wilke et al.   BMC BIOINFORMATICS

Measuring the microbiome: perspectives on advances in DNA-based techniques for exploring microbial life

(2012) J. A. Foster et al.   BRIEFINGS IN BIOINFORMATICS

A Platform-Independent Method for Detecting Errors in Metagenomic Sequencing Data: DRISEE

(2012) Kevin P. Keegan et al.   PLoS Computational Biology

RAPSearch: a fast protein similarity search tool for short reads

(2011) Yuzhen Ye et al.   BMC BIOINFORMATICS

Combining gene prediction methods to improve metagenomic gene annotation

(2011) Non G Yok et al.   BMC BIOINFORMATICS

CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing

(2011) Samuel V Angiuoli et al.   BMC BIOINFORMATICS

Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing

(2011) André Gilles et al.   BMC GENOMICS

IMG/M: the integrated metagenome data management and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

SmashCommunity: a metagenomic annotation and analysis tool: Fig. 1.

(2010) Manimozhiyan Arumugam et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

Unlocking Short Read Sequencing for Metagenomics

(2010) Sébastien Rodrigue et al.   PLoS One

The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data

(2010) David M. Tanenbaum et al.   Standards in Genomic Sciences

GENETACK: FRAMESHIFT IDENTIFICATION IN PROTEIN-CODING SEQUENCES BY THE VITERBI ALGORITHM

(2010) IVAN ANTONOV et al.   Journal of Bioinformatics and Computational Biology

Model-Based Quality Assessment and Base-Calling for Second-Generation Sequencing Data

(2009) Héctor Corrada Bravo et al.   BIOMETRICS

Gene prediction in metagenomic fragments: A large scale machine learning approach

(2009) Katharina J Hoff et al.   BMC BIOINFORMATICS

The effect of sequencing errors on metagenomic gene prediction

(2009) Katharina J Hoff   BMC GENOMICS

Next-generation gap

(2009) John D McPherson   NATURE METHODS

Metagenomics: Read Length Matters

(2008) K. E. Wommack et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Annotation of metagenome short reads using proxygenes

(2008) D. Dalevi et al.   BIOINFORMATICS

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

MetaGeneAnnotator: Detecting Species-Specific Patterns of Ribosomal Binding Site for Precise Gene Prediction in Anonymous Prokaryotic and Phage Genomes

(2008) H. Noguchi et al.   DNA RESEARCH

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

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