Published in Ecol Evol on January 12, 2017
QIIME allows analysis of high-throughput community sequencing data. Nat Methods (2010) 85.34
Biological identifications through DNA barcodes. Proc Biol Sci (2003) 54.14
Search and clustering orders of magnitude faster than BLAST. Bioinformatics (2010) 51.97
Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics (2012) 26.90
bold: The Barcode of Life Data System (http://www.barcodinglife.org). Mol Ecol Notes (2007) 25.13
UPARSE: highly accurate OTU sequences from microbial amplicon reads. Nat Methods (2013) 12.05
ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data. Bioinformatics (2009) 8.69
Integrative analysis of environmental sequences using MEGAN4. Genome Res (2011) 8.60
Monitoring endangered freshwater biodiversity using environmental DNA. Mol Ecol (2011) 3.45
Effect of primer mismatch, annealing temperature and PCR cycle number on 16S rRNA gene-targetting bacterial community analysis. FEMS Microbiol Ecol (2007) 3.34
Ocean plankton. Eukaryotic plankton diversity in the sunlit ocean. Science (2015) 3.04
Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene. FEMS Microbiol Ecol (2004) 2.88
New primers to amplify the fungal ITS2 region--evaluation by 454-sequencing of artificial and natural communities. FEMS Microbiol Ecol (2012) 2.83
Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Mol Ecol (2016) 1.85
Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Mol Ecol Resour (2015) 1.80
A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents. Front Zool (2013) 1.63
Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding. Ecol Lett (2013) 1.56
Using environmental DNA to census marine fishes in a large mesocosm. PLoS One (2014) 1.50
Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification. Gigascience (2013) 1.42
The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna. Proc Natl Acad Sci U S A (2012) 1.40
DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet. Mol Ecol Resour (2013) 1.39
ecoPrimers: inference of new DNA barcode markers from whole genome sequence analysis. Nucleic Acids Res (2011) 1.33
DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match. Biol Lett (2014) 1.33
DNA-based faecal dietary analysis: a comparison of qPCR and high throughput sequencing approaches. PLoS One (2011) 1.32
Quantification of diatom and dinoflagellate biomasses in coastal marine seawater samples by real-time PCR. Appl Environ Microbiol (2008) 1.31
Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data. Mol Ecol Resour (2014) 1.27
New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems. Mol Ecol (2012) 1.18
DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity. Proc Natl Acad Sci U S A (2015) 1.16
Next generation sequencing reveals the hidden diversity of zooplankton assemblages. PLoS One (2013) 1.13
Adélie penguin population diet monitoring by analysis of food DNA in scats. PLoS One (2013) 1.13
Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias. Mol Ecol Resour (2014) 1.08
Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods. Mol Ecol Resour (2014) 1.05
Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass--Sequence Relationships with an Innovative Metabarcoding Protocol. PLoS One (2015) 1.03
Performance comparison of genetic markers for high-throughput sequencing-based biodiversity assessment in complex communities. Mol Ecol Resour (2014) 0.98
Targeted gene enrichment and high-throughput sequencing for environmental biomonitoring: a case study using freshwater macroinvertebrates. Mol Ecol Resour (2015) 0.92
From benchtop to desktop: important considerations when designing amplicon sequencing workflows. PLoS One (2015) 0.90
Can abundance of protists be inferred from sequence data: a case study of foraminifera. PLoS One (2013) 0.88
A metagenetic approach for revealing community structure of marine planktonic copepods. Mol Ecol Resour (2014) 0.86
High-Throughput Sequencing-The Key to Rapid Biodiversity Assessment of Marine Metazoa? PLoS One (2015) 0.85
Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification. Sci Rep (2015) 0.82