Long-read DNA metabarcoding of ribosomal RNA in the analysis of fungi from aquatic environments

A Sequel to Sanger: amplicon sequencing that scales

(2018) Paul D. N. Hebert et al.   BMC GENOMICS

Metabarcoding analysis of eukaryotic microbiota in the gut of HIV-infected patients

(2018) Ibrahim Hamad et al.   PLoS One

Taxonomic annotation of public fungal ITS sequences from the built environment – a report from an April 10–11, 2017 workshop (Aberdeen, UK)

(2018) R. Henrik Nilsson et al.   MycoKeys

Reducing the impact of PCR-mediated recombination in molecular evolution and environmental studies using a new-generation high-fidelity DNA polymerase

(2018) Daniel J. G. Lahr et al.   BIOTECHNIQUES

Integrating chytrid fungal parasites into plankton ecology: research gaps and needs

(2017) Thijs Frenken et al.   ENVIRONMENTAL MICROBIOLOGY

Transformation of humic substances by the freshwater Ascomycete Cladosporium sp.

(2017) Keilor Rojas-Jimenez et al.   LIMNOLOGY AND OCEANOGRAPHY

PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives

(2017) Leho Tedersoo et al.   NEW PHYTOLOGIST

Community Profiling of Fusarium in Combination with Other Plant-Associated Fungi in Different Crop Species Using SMRT Sequencing

(2017) Florian Walder et al.   Frontiers in Plant Science

A comprehensive benchmarking study of protocols and sequencing platforms for 16S rRNA community profiling

(2016) Rosalinda D’Amore et al.   BMC GENOMICS

High-resolution phylogenetic microbial community profiling

(2016) Esther Singer et al.   ISME Journal

Characterization of pollen and bacterial community composition in brood provisions of a small carpenter bee

(2016) Quinn S. McFrederick et al.   MOLECULAR ECOLOGY

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

High-resolution community profiling of arbuscular mycorrhizal fungi

(2016) Klaus Schlaeppi et al.   NEW PHYTOLOGIST

Higher fungal diversity is correlated with lower CO2 emissions from dead wood in a natural forest

(2016) Chunyan Yang et al.   Scientific Reports

Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system

(2016) Patrick D. Schloss et al.   PeerJ

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany)

(2016) Christian Wurzbacher et al.   MycoKeys

Pitfalls of haplotype phasing from amplicon-based long-read sequencing

(2016) Thomas W. Laver et al.   Scientific Reports

Diversity and Distribution of Aquatic Fungal Communities in the Ny-Ålesund Region, Svalbard (High Arctic)

(2015) Tao Zhang et al.   MICROBIAL ECOLOGY

One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes

(2015) J.B. Stielow et al.   PERSOONIA

Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism

(2015) J. Davison et al.   SCIENCE

Micelle PCR reduces chimera formation in 16S rRNA profiling of complex microbial DNA mixtures

(2015) Stefan A. Boers et al.   Scientific Reports

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

(2015) Frédéric Mahé et al.   PeerJ

Improved OTU-picking using long-read 16S rRNA gene amplicon sequencing and generic hierarchical clustering

(2015) Oscar Franzén et al.   Microbiome

Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi

(2015) Leho Tedersoo et al.   MycoKeys

Lambda: the local aligner for massive biological data

(2014) Hannes Hauswedell et al.   BIOINFORMATICS

Where the wild things are: looking for uncultured Glomeromycota

(2014) Brian M. Ohsowski et al.   NEW PHYTOLOGIST

Importance of Saprotrophic Freshwater Fungi for Pollen Degradation

(2014) Christian Wurzbacher et al.   PLoS One

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

From Genus to Phylum: Large-Subunit and Internal Transcribed Spacer rRNA Operon Regions Show Similar Classification Accuracies Influenced by Database Composition

(2013) Andrea Porras-Alfaro et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

MHC genotyping of non-model organisms using next-generation sequencing: a new methodology to deal with artefacts and allelic dropout

(2013) Simone Sommer et al.   BMC GENOMICS

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

ITS1 versus ITS2 as DNA metabarcodes for fungi

(2013) R. Blaalid et al.   Molecular Ecology Resources

Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide

(2013) Björn D. Lindahl et al.   NEW PHYTOLOGIST

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

Metschnikowia Species Share a Pool of Diverse rRNA Genes Differing in Regions That Determine Hairpin-Loop Structures and Evolve by Reticulation

(2013) Matthias Sipiczki et al.   PLoS One

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

PCR inhibitors - occurrence, properties and removal

(2012) C. Schrader et al.   JOURNAL OF APPLIED MICROBIOLOGY

Effects of PCR cycle number and DNA polymerase type on the 16S rRNA gene pyrosequencing analysis of bacterial communities

(2012) Jae-Hyung Ahn et al.   JOURNAL OF MICROBIOLOGY

Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses

(2012) V. G. Fonseca 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

Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi

(2012) C. L. Schoch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DECIPHER, a Search-Based Approach to Chimera Identification for 16S rRNA Sequences

(2011) Erik S. Wright et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Exploring and quantifying fungal diversity in freshwater lake ecosystems using rDNA cloning/sequencing and SSU tag pyrosequencing

(2011) Sébastien Monchy et al.   ENVIRONMENTAL MICROBIOLOGY

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons?

(2011) Teresita M. Porter et al.   NEW PHYTOLOGIST

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

A flexible and efficient template format for circular consensus sequencing and SNP detection

(2010) K. J. Travers et al.   NUCLEIC ACIDS RESEARCH

Lobulomycetales, a new order in the Chytridiomycota

(2008) D. Rabern Simmons et al.