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

Application of DNA barcodes in wildlife conservation in Tropical East Asia

(2016) John-James Wilson et al.   CONSERVATION BIOLOGY

A quantitative protocol for DNA metabarcoding of springtails (Collembola)

(2016) Seikoh Saitoh et al.   GENOME

The sequence of sequencers: The history of sequencing DNA

(2016) James M. Heather et al.   GENOMICS

Long-term dynamics in microbial eukaryotes communities: a palaeolimnological view based on sedimentary DNA

(2016) Eric Capo et al.   MOLECULAR ECOLOGY

Fungal identification biases in microbiome projects

(2016) Leho Tedersoo et al.   Environmental Microbiology Reports

Comparison of three clustering approaches for detecting novel environmental microbial diversity

(2016) Dominik Forster et al.   PeerJ

Oomycete-specific ITS primers for identification and metabarcoding

(2016) Taavi Riit et al.   MycoKeys

BioMaS: a modular pipeline for Bioinformatic analysis of Metagenomic AmpliconS

(2015) Bruno Fosso et al.   BMC BIOINFORMATICS

Amplicon-Based Pyrosequencing Reveals High Diversity of Protistan Parasites in Ships’ Ballast Water: Implications for Biogeography and Infectious Diseases

(2015) K. M. Pagenkopp Lohan et al.   MICROBIAL ECOLOGY

metaxa2: improved identification and taxonomic classification of small and large subunit rRNA in metagenomic data

(2015) Johan Bengtsson-Palme et al.   Molecular Ecology Resources

obitools: aunix-inspired software package for DNA metabarcoding

(2015) Frédéric Boyer et al.   Molecular Ecology Resources

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

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

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data

(2015) Davide Albanese et al.   Scientific Reports

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

(2015) Jullien M. Flynn et al.   Ecology and Evolution

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

(2015) Sarah L. Westcott et al.   PeerJ

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

(2015) Frédéric Mahé et al.   PeerJ

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

(2015) Markus Majaneva et al.   PLoS One

Parsing ecological signal from noise in next generation amplicon sequencing

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

Global diversity and geography of soil fungi

(2014) L. Tedersoo et al.   SCIENCE

An Illumina metabarcoding pipeline for fungi

(2014) Miklós Bálint et al.   Ecology and Evolution

LotuS: an efficient and user-friendly OTU processing pipeline

(2014) Falk Hildebrand et al.   Microbiome

Analysis of soil fungal communities by amplicon pyrosequencing: current approaches to data analysis and the introduction of the pipeline SEED

(2013) Tomáš Větrovský et al.   BIOLOGY AND FERTILITY OF SOILS

The potential use of bacterial community succession in forensics as described by high throughput metagenomic sequencing

(2013) Jennifer L. Pechal et al.   INTERNATIONAL JOURNAL OF LEGAL MEDICINE

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

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

PyroClean: Denoising Pyrosequences from Protein-Coding Amplicons for the Recovery of Interspecific and Intraspecific Genetic Variation

(2013) Ricardo Ramirez-Gonzalez et al.   PLoS One

Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice

(2013) Falk Hildebrand et al.   GENOME BIOLOGY

CloVR-ITS: Automated internal transcribed spacer amplicon sequence analysis pipeline for the characterization of fungal microbiota

(2013) James Robert White et al.   Microbiome

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

(2012) Limin Fu et al.   BIOINFORMATICS

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

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

New environmental metabarcodes for analysing soil DNA: potential for studying past and present ecosystems

(2012) LAURA S. EPP et al.   MOLECULAR ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

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

(2011) T. Magoc et al.   BIOINFORMATICS

CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation

(2011) Surendra Kumar et al.   BMC BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   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

V-Xtractor: An open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16S/18S) ribosomal RNA gene sequences

(2010) Martin Hartmann et al.   JOURNAL OF MICROBIOLOGICAL METHODS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases

(2010) Leho Tedersoo et al.   NEW PHYTOLOGIST

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

(2009) Linda A. Amaral-Zettler et al.   PLoS One