Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data

Probing promise versus performance in longer read fungal metabarcoding

(2018) Peter G. Kennedy et al.   NEW PHYTOLOGIST

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

(2017) Leho Tedersoo et al.   NEW PHYTOLOGIST

Evaluating the Impact of DNA Extraction Method on the Representation of Human Oral Bacterial and Fungal Communities

(2017) Anna Vesty et al.   PLoS One

Accurate Estimation of Fungal Diversity and Abundance through Improved Lineage-Specific Primers Optimized for Illumina Amplicon Sequencing

(2016) D. Lee Taylor et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quality filtering of Illumina index reads mitigates sample cross-talk

(2016) Erik Scott Wright et al.   BMC GENOMICS

FUNGuild: An open annotation tool for parsing fungal community datasets by ecological guild

(2016) Nhu H. Nguyen et al.   Fungal Ecology

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing

(2016) Dieter M. Tourlousse et al.   NUCLEIC ACIDS RESEARCH

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Identification of Putative Coffee Rust Mycoparasites via Single-Molecule DNA Sequencing of Infected Pustules

(2015) Timothy Y. James et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2015) Robert C. Edgar et al.   BIOINFORMATICS

Polymerase matters: non-proofreading enzymes inflate fungal community richness estimates by up to 15 %

(2015) Alena K. Oliver et al.   Fungal Ecology

Tag jumps illuminated - reducing sequence-to-sample misidentifications in metabarcoding studies

(2015) Ida Baerholm Schnell et al.   Molecular Ecology Resources

Navigating the labyrinth: a guide to sequence-based, community ecology of arbuscular mycorrhizal fungi

(2015) Miranda M. Hart et al.   NEW PHYTOLOGIST

Accurate multiplexing and filtering for high-throughput amplicon-sequencing

(2015) Philippe Esling et al.   NUCLEIC ACIDS RESEARCH

Sources of PCR-induced distortions in high-throughput sequencing data sets

(2015) Justus M. Kebschull et al.   NUCLEIC ACIDS RESEARCH

PIPITS: an automated pipeline for analyses of fungal internal transcribed spacer sequences from the Illumina sequencing platform

(2015) Hyun S. Gweon et al.   Methods in Ecology and Evolution

ITS1: a DNA barcode better than ITS2 in eukaryotes?

(2014) Xin-Cun Wang et al.   Molecular Ecology Resources

Parsing ecological signal from noise in next generation amplicon sequencing

(2014) Nhu H. Nguyen et al.   NEW PHYTOLOGIST

Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing

(2014) Dylan P. Smith et al.   PLoS One

Amplicon –Based Metagenomic Analysis of Mixed Fungal Samples Using Proton Release Amplicon Sequencing

(2014) Daniel P. Tonge et al.   PLoS One

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

(2014) C. L. Schoch et al.   Database-The Journal of Biological Databases and Curation

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data

(2013) Johan Bengtsson-Palme et al.   Methods in Ecology and Evolution

New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities

(2012) Katarina Ihrmark et al.   FEMS MICROBIOLOGY ECOLOGY

Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies?

(2012) Tor Carlsen et al.   Fungal Ecology

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets

(2012) Ameet J. Pinto et al.   PLoS One

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome

(2012) Daniel McDonald et al.   GigaScience

Addressing challenges in the production and analysis of illumina sequencing data

(2011) Martin Kircher et al.   BMC GENOMICS

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Nuclear and Genome Dynamics in Multinucleate Ascomycete Fungi

(2011) Marcus Roper et al.   CURRENT BIOLOGY

Illumina-based analysis of microbial community diversity

(2011) Patrick H Degnan et al.   ISME Journal

Intragenomic variation in the ITS rDNA region obscures phylogenetic relationships and inflates estimates of operational taxonomic units in genus Laetiporus

(2011) Daniel L. Lindner et al.   MYCOLOGIA

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Effects of polymerase, template dilution and cycle number on PCR based 16 S rRNA diversity analysis using the deep sequencing method

(2010) Jin-Ya Wu et al.   BMC MICROBIOLOGY

Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

(2010) ANTHONY S. AMEND et al.   MOLECULAR ECOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

The UNITE database for molecular identification of fungi - recent updates and future perspectives

(2010) Kessy Abarenkov et al.   NEW PHYTOLOGIST

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

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

(2009) M. Morgan et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Intragenomic Variation of Fungal Ribosomal Genes Is Higher than Previously Thought

(2008) U. K. Simon et al.   MOLECULAR BIOLOGY AND EVOLUTION

Molecular phylogeny of Laetiporus and other brown rot polypore genera in North America

(2008) Daniel L. Lindner et al.   MYCOLOGIA