Ultrafast clustering algorithms for metagenomic sequence analysis

KABOOM! A new suffix array based algorithm for clustering expression data

(2011) Scott Hazelhurst et al.   BIOINFORMATICS

SEED: efficient clustering of next-generation sequences

(2011) Ergude Bao et al.   BIOINFORMATICS

Error correction of high-throughput sequencing datasets with non-uniform coverage

(2011) P. Medvedev et al.   BIOINFORMATICS

FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes

(2011) Beifang Niu et al.   BIOINFORMATICS

DNACLUST: accurate and efficient clustering of phylogenetic marker genes

(2011) Mohammadreza Ghodsi et al.   BMC BIOINFORMATICS

RAPSearch: a fast protein similarity search tool for short reads

(2011) Yuzhen Ye et al.   BMC BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

WebMGA: a customizable web server for fast metagenomic sequence analysis

(2011) Sitao Wu et al.   BMC GENOMICS

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis

(2011) Y. Sun et al.   BRIEFINGS IN BIOINFORMATICS

ECHO: A reference-free short-read error correction algorithm

(2011) W.-C. Kao et al.   GENOME RESEARCH

A decade’s perspective on DNA sequencing technology

(2011) Elaine R. Mardis   NATURE

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

(2011) Hamidreza Chitsaz et al.   NATURE BIOTECHNOLOGY

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

(2011) M. Hess et al.   SCIENCE

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Artificial and natural duplicates in pyrosequencing reads of metagenomic data

(2010) Beifang Niu et al.   BMC BIOINFORMATICS

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

EDAR: An Efficient Error Detection and Removal Algorithm for Next Generation Sequencing Data

(2010) Xiaohong Zhao et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Rapidly denoising pyrosequencing amplicon reads by exploiting rank-abundance distributions

(2010) Jens Reeder et al.   NATURE METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource

(2010) S. Sun et al.   NUCLEIC ACIDS RESEARCH

Comparison of sequence profiles. Strategies for structural predictions using sequence information

(2010) Leszek Rychlewski et al.   PROTEIN SCIENCE

A Primer on Metagenomics

(2010) John C. Wooley et al.   PLoS Computational Biology

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

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Analysis and comparison of very large metagenomes with fast clustering and functional annotation

(2009) Weizhong Li   BMC BIOINFORMATICS

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

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing

(2009) W. Qu et al.   GENOME RESEARCH

De novo assembly of human genomes with massively parallel short read sequencing

(2009) R. Li et al.   GENOME RESEARCH

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Systematic artifacts in metagenomes from complex microbial communities

(2009) Vicente Gomez-Alvarez et al.   ISME Journal

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences

(2009) Yijun Sun et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space

(2008) Y. Loewenstein et al.   BIOINFORMATICS

Gene identification and protein classification in microbial metagenomic sequence data via incremental clustering

(2008) Shibu Yooseph et al.   BMC BIOINFORMATICS

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

(2008) F Meyer et al.   BMC BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Functional metagenomic profiling of nine biomes

(2008) Elizabeth A. Dinsdale et al.   NATURE

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities

(2008) Jack A. Gilbert et al.   PLoS One

Probing Metagenomics by Rapid Cluster Analysis of Very Large Datasets

(2008) Weizhong Li et al.   PLoS One