Swarm v2: highly-scalable and high-resolution amplicon clustering

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

Determinants of community structure in the global plankton interactome

(2015) G. Lima-Mendez et al.   SCIENCE

Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?

(2015) Emily A. Brown et al.   Ecology and Evolution

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

Protistan diversity in a permanently stratified meromictic lake (Lake Alatsee, SW Germany)

(2014) Andreas Oikonomou et al.   ENVIRONMENTAL MICROBIOLOGY

Deep sequencing uncovers protistan plankton diversity in the Portuguese Ria Formosa solar saltern ponds

(2014) Sabine Filker et al.   EXTREMOPHILES

Comparing High-throughput Platforms for Sequencing the V4 Region of SSU-rDNA in Environmental Microbial Eukaryotic Diversity Surveys

(2014) Frédéric Mahé et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

(2014) Jai Ram Rideout et al.   PeerJ

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

(2014) Frédéric Mahé et al.   PeerJ

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

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

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests

(2012) Martin Hartmann et al.   ISME Journal

Comparing the Hyper-Variable V4 and V9 Regions of the Small Subunit rDNA for Assessment of Ciliate Environmental Diversity

(2012) Micah Dunthorn et al.   JOURNAL OF EUKARYOTIC MICROBIOLOGY

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

(2012) Laure Guillou et al.   NUCLEIC ACIDS RESEARCH

DNACLUST: accurate and efficient clustering of phylogenetic marker genes

(2011) Mohammadreza Ghodsi et al.   BMC BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions

(2010) Anke Behnke et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Delimiting operational taxonomic units for assessing ciliate environmental diversity using small-subunit rRNA gene sequences

(2010) Markus Nebel et al.   Environmental Microbiology Reports

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Defining DNA-Based Operational Taxonomic Units for Microbial-Eukaryote Ecology

(2009) D. A. Caron 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