Method for quick DNA barcode reference library construction

A method to generate multilocus barcodes of pinned insect specimens using MiSeq

(2020) Trace Akankunda et al.   Molecular Ecology Resources

Rapid and cost-effective generation of single specimen multilocus barcoding data from whole arthropod communities by multiple levels of multiplexing

(2020) Guillemette A. de Kerdrel et al.   Scientific Reports

Comparison of Illumina MiSeq and the Ion Torrent PGM and S5 platforms for whole-genome sequencing of picornaviruses and caliciviruses

(2020) Rachel L. Marine et al.   JOURNAL OF VIROLOGICAL METHODS

An efficient and cost-effective method for primer-induced nucleotide labeling for massive sequencing on next-generation sequencing platforms

(2019) Junjie Guo et al.   Scientific Reports

A validated workflow for rapid taxonomic assignment and monitoring of a national fauna of bees (Apiformes) using high throughput DNA barcoding

(2019) Thomas J. Creedy et al.   Molecular Ecology Resources

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Identification of Indian Spiders through DNA barcoding: Cryptic species and species complex

(2019) Kaomud Tyagi et al.   Scientific Reports

Genetic Biomonitoring and Biodiversity Assessment Using Portable Sequencing Technologies: Current Uses and Future Directions

(2019) Krehenwinkel et al.   Genes

Parallelization of MAFFT for large-scale multiple sequence alignments

(2018) Tsukasa Nakamura et al.   BIOINFORMATICS

Updating the 97% identity threshold for 16S ribosomal RNA OTUs

(2018) Robert C Edgar   BIOINFORMATICS

Comparative analysis of Illumina and Ion Torrent high-throughput sequencing platforms for identification of plant components in herbal teas

(2018) Anna S. Speranskaya et al.   FOOD CONTROL

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

A MinION™-based pipeline for fast and cost-effective DNA barcoding

(2018) Amrita Srivathsan et al.   Molecular Ecology Resources

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Identification of species adulteration in traded medicinal plant raw drugs using DNA barcoding

(2017) Stalin Nithaniyal et al.   GENOME

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

FuzzyID2: A software package for large data set species identification via barcoding and metabarcoding using hidden Markov models and fuzzy set methods

(2017) Zhi-yong Shi et al.   Molecular Ecology Resources

DNA barcoding of invasive plants in China: A resource for identifying invasive plants

(2017) Song-Zhi Xu et al.   Molecular Ecology Resources

PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data

(2017) Sten Anslan et al.   Molecular Ecology Resources

Five thousand years of tropical lake sediment DNA records from Benin

(2017) L. Bremond et al.   QUATERNARY SCIENCE REVIEWS

Plant DNA barcodes: Applications today and in the future

(2017) W. John Kress   Journal of Systematics and Evolution

Utility of DNA barcoding to identify rare endemic vascular plant species in Trinidad

(2017) Fazeeda N. Hosein et al.   Ecology and Evolution

DNA metabarcoding for diet analysis and biodiversity: A case study using the endangered Australian sea lion (Neophoca cinerea )

(2017) Tina E. Berry et al.   Ecology and Evolution

Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea

(2017) Satoshi Yamamoto et al.   Scientific Reports

Detection of mislabelled seafood products in Malaysia by DNA barcoding: Improving transparency in food market

(2016) Too Chin Chin et al.   FOOD CONTROL

DNA barcoding of fungi causing infections in humans and animals

(2016) Laszlo Irinyi et al.   Fungal Biology

Evaluating and optimizing the performance of software commonly used for the taxonomic classification of DNA metabarcoding sequence data

(2016) Rodney T. Richardson et al.   Molecular Ecology Resources

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

DNA barcoding reveals a mysterious high species diversity of conifer-feeding aphids in the mountains of southwest China

(2016) Rui Chen et al.   Scientific Reports

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

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

(2015) Robert C. Edgar et al.   BIOINFORMATICS

Accelerating plant DNA barcode reference library construction using herbarium specimens: improved experimental techniques

(2015) Chao Xu et al.   Molecular Ecology Resources

Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding

(2015) Nathan T. Evans et al.   Molecular Ecology Resources

obitools: aunix-inspired software package for DNA metabarcoding

(2015) Frédéric Boyer et al.   Molecular Ecology Resources

High-throughput DNA barcoding for ecological network studies

(2015) Hirokazu Toju   POPULATION ECOLOGY

DNA metabarcoding illuminates dietary niche partitioning by African large herbivores

(2015) Tyler R. Kartzinel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Continental-scale distributions of dust-associated bacteria and fungi

(2015) Albert Barberán et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ycf1, the most promising plastid DNA barcode of land plants

(2015) Wenpan Dong et al.   Scientific Reports

Performance Comparison of Illumina and Ion Torrent Next-Generation Sequencing Platforms for 16S rRNA-Based Bacterial Community Profiling

(2014) Stephen J. Salipante et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens

(2014) Shadi Shokralla et al.   Molecular Ecology Resources

Evaluation of the DNA barcoding approach to develop a reference data-set for the threatened flora of Sicily

(2014) A. Giovino et al.   PLANT BIOSYSTEMS

Discriminating plants using the DNA barcoderbcLb: an appraisal based on a large data set

(2013) Wenpan Dong et al.   Molecular Ecology Resources

Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?

(2013) Bruce E. Deagle et al.   Molecular Ecology Resources

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Illumina metabarcoding of a soil fungal community

(2013) Philipp-André Schmidt et al.   SOIL BIOLOGY & BIOCHEMISTRY

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Next-generation sequencing technologies for environmental DNA research

(2012) SHADI SHOKRALLA et al.   MOLECULAR ECOLOGY

|SE|S|AM|E| Barcode: NGS-oriented software for amplicon characterization - application to species and environmental barcoding

(2012) S. PIRY et al.   Molecular Ecology Resources

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Environmental Barcoding: A Next-Generation Sequencing Approach for Biomonitoring Applications Using River Benthos

(2011) Mehrdad Hajibabaei et al.   PLoS One

Choosing and Using a Plant DNA Barcode

(2011) Peter M. Hollingsworth et al.   PLoS One

Comparative analysis of a large dataset indicates that internal transcribed spacer (ITS) should be incorporated into the core barcode for seed plants

(2011) et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New universal matK primers for DNA barcoding angiosperms

(2011) Jing YU et al.   Journal of Systematics and Evolution

How Many Species Are There on Earth and in the Ocean?

(2011) Camilo Mora et al.   PLOS 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

A DNA barcode for land plants

(2009) et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA