VSEARCH: a versatile open source tool for metagenomics

Application of a Database-Independent Approach To Assess the Quality of Operational Taxonomic Unit Picking Methods

(2016) Patrick D. Schloss   mSystems

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

Planetary boundaries: Guiding human development on a changing planet

(2015) W. Steffen et al.   SCIENCE

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

Stability of operational taxonomic units: an important but neglected property for analyzing microbial diversity

(2015) Yan He et al.   Microbiome

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

Patterns of Rare and Abundant Marine Microbial Eukaryotes

(2014) Ramiro Logares et al.   CURRENT BIOLOGY

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

(2014) Frédéric Mahé et al.   PeerJ

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing

(2013) K. Song et al.   BRIEFINGS IN BIOINFORMATICS

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

(2011) Torbjørn Rognes   BMC BIOINFORMATICS

A Holistic Approach to Marine Eco-Systems Biology

(2011) Eric Karsenti et al.   PLOS BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

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

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A safe operating space for humanity

(2009) Johan Rockström et al.   NATURE

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

(2009) Peter J. A. Cock et al.   NUCLEIC ACIDS RESEARCH

ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads

(2009) Iain MacCallum et al.   GENOME BIOLOGY