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Andreas Makiola et al.
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ITSoneDB: a comprehensive collection of eukaryotic ribosomal RNA Internal Transcribed Spacer 1 (ITS1) sequences
Monica Santamaria et al.
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SEED 2: a user-friendly platform for amplicon high-throughput sequencing data analyses
Tomas Vetrovsky et al.
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David Garcia de Leon et al.
GLOBAL CHANGE BIOLOGY (2018)
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Ylva Lekberg et al.
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Fungal microbiota dysbiosis in IBD
Harry Sokol et al.
GUT (2017)
ITS all right mama: investigating the formation of chimeric sequences in the ITS2 region by DNA metabarcoding analyses of fungal mock communities of different complexities
Anders Bjornsgaard Aas et al.
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UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy
Tom Smith et al.
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PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data
Sten Anslan et al.
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Martti Vasar et al.
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A communal catalogue reveals Earth's multiscale microbial diversity
Luke R. Thompson et al.
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BARCODED NS31/AML2 PRIMERS FOR SEQUENCING OF ARBUSCULAR MYCORRHIZAL COMMUNITIES IN ENVIRONMENTAL SAMPLES
Benjamin S. T. Morgan et al.
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Novel soil-inhabiting clades fill gaps in the fungal tree of life
Leho Tedersoo et al.
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Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory
R. Henrik Nilsson et al.
MYCOKEYS (2017)
Evaluation of the reproducibility of amplicon sequencing with Illumina MiSeq platform
Chongqing Wen et al.
PLOS ONE (2017)
Denoising DNA deep sequencing data-high-throughput sequencing errors and their correction
David Laehnemann et al.
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The International Nucleotide Sequence Database Collaboration
Guy Cochrane et al.
NUCLEIC ACIDS RESEARCH (2016)
Phylogenetically Structured Differences in rRNA Gene Sequence Variation among Species of Arbuscular Mycorrhizal Fungi and Their Implications for Sequence Clustering
Geoffrey L. House et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2016)
High-resolution phylogenetic microbial community profiling
Esther Singer et al.
ISME JOURNAL (2016)
DADA2: High-resolution sample inference from Illumina amplicon data
Benjamin J. Callahan et al.
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Efficiency of matK, rbcL, trnH-psbA, and trnL-F (cpDNA) to Molecularly Authenticate Philippine Ethnomedicinal Apocynaceae Through DNA Barcoding
Vincent Louie Domingo Cabelin et al.
PHARMACOGNOSY MAGAZINE (2016)
Sequencing 16S rRNA gene fragments using the PacBio SMRT DNA sequencing system
Patrick D. Schloss et al.
PEERJ (2016)
VSEARCH: a versatile open source tool for metagenomics
Torbjorn Rognes et al.
PEERJ (2016)
A three-marker DNA barcoding approach for ecological studies of xerothermic plants and herbivorous insects from central Europe
Waldemar Heise et al.
BOTANICAL JOURNAL OF THE LINNEAN SOCIETY (2015)
Scraping the bottom of the barrel: are rare high throughput sequences artifacts?
Shawn P. Brown et al.
FUNGAL ECOLOGY (2015)
Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform
Melanie Schirmer et al.
NUCLEIC ACIDS RESEARCH (2015)
Global assessment of arbuscular mycorrhizal fungus diversity reveals very low endemism
J. Davison et al.
SCIENCE (2015)
De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units
Sarah L. Westcott et al.
PEERJ (2015)
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
Jiajie Zhang et al.
BIOINFORMATICS (2014)
Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities
Ramiro Logares et al.
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Regional Effects on Chimera Formation in 454 Pyrosequenced Amplicons from a Mock Community
Sunguk Shin et al.
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Effects of long-term differential fertilization on eukaryotic microbial communities in an arable soil: a multiple barcoding approach
Guillaume Lentendu et al.
MOLECULAR ECOLOGY (2014)
Characterization of the 18S rRNA Gene for Designing Universal Eukaryote Specific Primers
Kenan Hadziavdic et al.
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Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys
Michael C. Nelson et al.
PLOS ONE (2014)
Comparison of commonly used primer sets for evaluating arbuscular mycorrhizal fungal communities: Is there a universal solution?
Petr Kohout et al.
SOIL BIOLOGY & BIOCHEMISTRY (2014)
An Illumina metabarcoding pipeline for fungi
Miklos Balint et al.
ECOLOGY AND EVOLUTION (2014)
Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform
James J. Kozich et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2013)
Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide
Bjorn D. Lindahl et al.
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Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
Nicholas A. Bokulich et al.
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The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
Christian Quast et al.
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New primers to amplify the fungal ITS2 region - evaluation by 454-sequencing of artificial and natural communities
Katarina Ihrmark et al.
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Plant species richness belowground: higher richness and new patterns revealed by next-generation sequencing
Inga Hiiesalu et al.
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Towards next-generation biodiversity assessment using DNA metabarcoding
Pierre Taberlet et al.
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Quality-Score Refinement of SSU rRNA Gene Pyrosequencing Differs Across Gene Region for Environmental Samples
Kara Bowen De Leon et al.
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PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution
Stephane Mahe et al.
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Cultivation of unculturable soil bacteria
Van H. T. Pham et al.
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Sequencing our way towards understanding global eukaryotic biodiversity
Holly M. Bik et al.
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UCHIME improves sensitivity and speed of chimera detection
Robert C. Edgar et al.
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FLASH: fast length adjustment of short reads to improve genome assemblies
Tanja Magoc et al.
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Distinct seasonal assemblages of arbuscular mycorrhizal fungi revealed by massively parallel pyrosequencing
Alex J. Dumbrell et al.
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Tidying Up International Nucleotide Sequence Databases: Ecological, Geographical and Sequence Quality Annotation of ITS Sequences of Mycorrhizal Fungi
Leho Tedersoo et al.
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Patrick D. Schloss et al.
PLOS ONE (2011)
Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
Victor Kunin et al.
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An open source chimera checker for the fungal ITS region
R. H. Nilsson et al.
MOLECULAR ECOLOGY RESOURCES (2010)
QIIME allows analysis of high-throughput community sequencing data
J. Gregory Caporaso et al.
NATURE METHODS (2010)
The online database MaarjAM reveals global and ecosystemic distribution patterns in arbuscular mycorrhizal fungi (Glomeromycota)
M. Opik et al.
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454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases
Leho Tedersoo et al.
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The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
Peter J. A. Cock et al.
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Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
Patrick D. Schloss et al.
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BLAST plus : architecture and applications
Christiam Camacho et al.
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Large-scale parallel 454 sequencing reveals host ecological group specificity of arbuscular mycorrhizal fungi in a boreonemoral forest
M. Oepik et al.
NEW PHYTOLOGIST (2009)
Improved PCR primers for the detection and identification of arbuscular mycorrhizal fungi
Jaikoo Lee et al.
FEMS MICROBIOLOGY ECOLOGY (2008)
Biological identifications through DNA barcodes
PDN Hebert et al.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2003)
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