Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding

SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses

(2018) Tomáš Větrovský et al.   BIOINFORMATICS

Seasonal and annual variation in fungal communities associated with epigeic springtails (Collembola spp.) in boreal forests

(2018) Sten Anslan et al.   SOIL BIOLOGY & BIOCHEMISTRY

Sequence-based nomenclature: a reply to Thines et al. and Zamora et al. and provisions for an amended proposal "from the floor" to allow DNA sequences as types of names

(2018) Robert Lücking et al.   IMA Fungus

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

(2017) Sten Anslan et al.   Molecular Ecology Resources

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium

(2017) Rashmi Sinha et al.   NATURE BIOTECHNOLOGY

Moving beyond de novo clustering in fungal community ecology

(2017) Lauren C. Cline et al.   NEW PHYTOLOGIST

Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

(2017) Tobias Guldberg Frøslev et al.   Nature Communications

Discovery of dark matter fungi in aquatic ecosystems demands a reappraisal of the phylogeny and ecology of zoosporic fungi

(2016) Hans-Peter Grossart et al.   Fungal Ecology

Fungal identification using a Bayesian classifier and the Warcup training set of internal transcribed spacer sequences

(2016) Vinita Deshpande et al.   MYCOLOGIA

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Scraping the bottom of the barrel: are rare high throughput sequences artifacts?

(2015) Shawn P. Brown et al.   Fungal Ecology

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

Bioinformatic Amplicon Read Processing Strategies Strongly Affect Eukaryotic Diversity and the Taxonomic Composition of Communities

(2015) Markus Majaneva et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

LotuS: an efficient and user-friendly OTU processing pipeline

(2014) Falk Hildebrand et al.   Microbiome

PERMANOVA, ANOSIM, and the Mantel test in the face of heterogeneous dispersions: What null hypothesis are you testing?

(2013) Marti J. Anderson et al.   ECOLOGICAL MONOGRAPHS

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

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

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

(2012) Limin Fu et al.   BIOINFORMATICS

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

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Manipulation of FASTQ data with Galaxy

(2010) D. Blankenberg et al.   BIOINFORMATICS

PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences

(2010) Kessy Abarenkov et al.   Evolutionary Bioinformatics

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS