To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography
出版年份 2021 全文链接
标题
To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography
作者
关键词
-
出版物
BMC BIOINFORMATICS
Volume 22, Issue 1, Pages -
出版商
Springer Science and Business Media LLC
发表日期
2021-04-05
DOI
10.1186/s12859-021-04115-6
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Testing small‐scale ecological gradients and intraspecific differentiation for hundreds of kelp forest species using haplotypes from metabarcoding
- (2021) Peter Shum et al. MOLECULAR ECOLOGY
- Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data
- (2021) Carmelo Andújar et al. Molecular Ecology Resources
- Environmental DNA surveys detect distinct metazoan communities across abyssal plains and seamounts in the western Clarion Clipperton Zone
- (2020) Olivier Laroche et al. MOLECULAR ECOLOGY
- Comparing diversity levels in environmental samples: DNA sequence capture and metabarcoding approaches using 18S and COI genes
- (2020) H Giebner et al. Molecular Ecology Resources
- Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape
- (2020) Bryan N. Nguyen et al. Scientific Reports
- A Systematic Review of Sources of Variability and Uncertainty in eDNA Data for Environmental Monitoring
- (2020) Chloé Mathieu et al. Frontiers in Ecology and Evolution
- AmpliCI: A High-resolution Model-Based Approach for Denoising Illumina Amplicon Data
- (2020) Xiyu Peng et al. BIOINFORMATICS
- Advances in metabarcoding techniques bring us closer to reliable monitoring of the marine benthos
- (2020) Margaux Steyaert et al. JOURNAL OF APPLIED ECOLOGY
- Biases in bulk: DNA metabarcoding of marine communities and the methodology involved
- (2020) Luna M. van der Loos et al. MOLECULAR ECOLOGY
- Reconstructing marine plankton food web interactions using DNA metabarcoding
- (2020) Sara Zamora‐Terol et al. MOLECULAR ECOLOGY
- A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses
- (2020) Devon R. O'Rourke et al. Ecology and Evolution
- Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis
- (2020) Teresita M. Porter et al. Frontiers in Ecology and Evolution
- Pan‐regional marine benthic cryptobiome biodiversity patterns revealed by metabarcoding Autonomous Reef Monitoring Structures
- (2020) J.K. Pearman et al. MOLECULAR ECOLOGY
- Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities?
- (2020) Adrià Antich et al. MOLECULAR ECOLOGY
- Metabarcoding From Microbes to Mammals: Comprehensive Bioassessment on a Global Scale
- (2020) Zacchaeus G. Compson et al. Frontiers in Ecology and Evolution
- Metabarcoding free‐living marine nematodes using curated 18S and CO1 reference sequence databases for species‐level taxonomic assignments
- (2019) Lara Macheriotou et al. Ecology and Evolution
- Improving eDNA‐based protist diversity assessments using networks of amplicon sequence variants
- (2019) Dominik Forster et al. ENVIRONMENTAL MICROBIOLOGY
- Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
- (2019) Evan Bolyen et al. NATURE BIOTECHNOLOGY
- DNA metabarcoding reveals modern and past eukaryotic communities in a high-mountain peat bog system
- (2019) Sandra Garcés-Pastor et al. JOURNAL OF PALEOLIMNOLOGY
- Diatom DNA Metabarcoding for Biomonitoring: Strategies to Avoid Major Taxonomical and Bioinformatical Biases Limiting Molecular Indices Capacities
- (2019) Kálmán Tapolczai et al. Frontiers in Ecology and Evolution
- From metabarcoding to metaphylogeography: separating the wheat from the chaff
- (2019) Xavier Turon et al. ECOLOGICAL APPLICATIONS
- Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding
- (2019) Judith Bakker et al. Ecology and Evolution
- Estimating intraspecific genetic diversity from community DNA metabarcoding data
- (2018) Vasco Elbrecht et al. PeerJ
- DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers
- (2018) Owen S. Wangensteen et al. PeerJ
- Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks
- (2018) Eva Aylagas et al. ECOLOGICAL INDICATORS
- Why the COI barcode should be the community DNA metabarcode for the metazoa
- (2018) Carmelo Andújar et al. MOLECULAR ECOLOGY
- Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches
- (2018) Jacob T. Nearing et al. PeerJ
- Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring
- (2018) Andjin Siegenthaler et al. Molecular Ecology Resources
- Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
- (2017) Benjamin J Callahan et al. ISME Journal
- Environmental DNA metabarcoding: Transforming how we survey animal and plant communities
- (2017) Kristy Deiner et al. MOLECULAR ECOLOGY
- Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
- (2017) Amnon Amir et al. mSystems
- DADA2: High-resolution sample inference from Illumina amplicon data
- (2016) Benjamin J Callahan et al. NATURE METHODS
- VSEARCH: a versatile open source tool for metagenomics
- (2016) Torbjørn Rognes et al. PeerJ
- Open-Source Sequence Clustering Methods Improve the State Of the Art
- (2016) Evguenia Kopylova et al. mSystems
- Molecular evolution of a widely-adopted taxonomic marker (COI) across the animal tree of life
- (2016) Mikko Pentinsaari et al. Scientific Reports
- obitools: aunix-inspired software package for DNA metabarcoding
- (2015) Frédéric Boyer et al. Molecular Ecology Resources
- Swarm v2: highly-scalable and high-resolution amplicon clustering
- (2015) Frédéric Mahé et al. PeerJ
- Swarm: robust and fast clustering method for amplicon-based studies
- (2014) Frédéric Mahé et al. PeerJ
- UPARSE: highly accurate OTU sequences from microbial amplicon reads
- (2013) Robert C Edgar NATURE METHODS
- Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering
- (2011) Xiaolin Hao et al. BIOINFORMATICS
- Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities
- (2011) B. C. Emerson et al. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
- Search and clustering orders of magnitude faster than BLAST
- (2010) Robert C. Edgar BIOINFORMATICS
- Phylogeography: retrospect and prospect
- (2008) John C. Avise JOURNAL OF BIOGEOGRAPHY
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