From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows
Published 2015 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows
Authors
Keywords
-
Journal
PLoS One
Volume 10, Issue 4, Pages e0124671
Publisher
Public Library of Science (PLoS)
Online
2015-04-23
DOI
10.1371/journal.pone.0124671
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match
- (2014) B. E. Deagle et al. Biology Letters
- Next-generation sequencing reveals large connected networks of intra-host HCV variants
- (2014) David S Campo et al. BMC GENOMICS
- Identifying conservation units after large-scale land clearing: a spatio-temporal molecular survey of endangered white-tailed black cockatoos (Calyptorhynchusspp.)
- (2014) Nicole E. White et al. DIVERSITY AND DISTRIBUTIONS
- Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill
- (2014) Olivia U Mason et al. ISME Journal
- Fifty thousand years of Arctic vegetation and megafaunal diet
- (2014) Eske Willerslev et al. NATURE
- Dynamics and associations of microbial community types across the human body
- (2014) Tao Ding et al. NATURE
- Sequence Depth, Not PCR Replication, Improves Ecological Inference from Next Generation DNA Sequencing
- (2014) Dylan P. Smith et al. PLoS One
- High throughput sequencing analysis of biogeographical distribution of bacterial communities in the black soils of northeast China
- (2014) Junjie Liu et al. SOIL BIOLOGY & BIOCHEMISTRY
- A long-term field experiment of soil transplantation demonstrating the role of contemporary geographic separation in shaping soil microbial community structure
- (2014) Bo Sun et al. Ecology and Evolution
- Who's for dinner? High-throughput sequencing reveals bat dietary differentiation in a biodiversity hotspot where prey taxonomy is largely undescribed
- (2013) Joanna M. Burgar et al. MOLECULAR ECOLOGY
- Modular tagging of amplicons using a single PCR for high-throughput sequencing
- (2013) Laurence J. Clarke et al. Molecular Ecology Resources
- Amplicon pyrosequencing late Pleistocene permafrost: the removal of putative contaminant sequences and small-scale reproducibility
- (2013) Teresita M. Porter et al. Molecular Ecology Resources
- DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet
- (2013) M. De Barba et al. Molecular Ecology Resources
- UPARSE: highly accurate OTU sequences from microbial amplicon reads
- (2013) Robert C Edgar NATURE METHODS
- The role of replicates for error mitigation in next-generation sequencing
- (2013) Kimberly Robasky et al. NATURE REVIEWS GENETICS
- A DNA Metabarcoding Study of a Primate Dietary Diversity and Plasticity across Its Entire Fragmented Range
- (2013) Erwan Quéméré et al. PLoS One
- Effects of GC Bias in Next-Generation-Sequencing Data on De Novo Genome Assembly
- (2013) Yen-Chun Chen et al. PLoS One
- Scrapheap Challenge: A novel bulk-bone metabarcoding method to investigate ancient DNA in faunal assemblages
- (2013) Dáithí C. Murray et al. Scientific Reports
- Characterizing and measuring bias in sequence data
- (2013) Michael G Ross et al. GENOME BIOLOGY
- Significant changes in the skin microbiome mediated by the sport of roller derby
- (2013) James F. Meadow et al. PeerJ
- Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries
- (2012) Jesse Dabney et al. BIOTECHNIQUES
- A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers
- (2012) Michael Quail et al. BMC GENOMICS
- Evaluation and optimisation of preparative semi-automated electrophoresis systems for Illumina library preparation
- (2012) Michael A. Quail et al. ELECTROPHORESIS
- Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing
- (2012) DONALD J. BAIRD et al. MOLECULAR ECOLOGY
- Next-generation sequencing technologies for environmental DNA research
- (2012) SHADI SHOKRALLA et al. MOLECULAR ECOLOGY
- Towards next-generation biodiversity assessment using DNA metabarcoding
- (2012) PIERRE TABERLET et al. MOLECULAR ECOLOGY
- An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding
- (2012) H. R. TAYLOR et al. Molecular Ecology Resources
- |SE|S|AM|E| Barcode: NGS-oriented software for amplicon characterization - application to species and environmental barcoding
- (2012) S. PIRY et al. Molecular Ecology Resources
- Performance comparison of benchtop high-throughput sequencing platforms
- (2012) Nicholas J Loman et al. NATURE BIOTECHNOLOGY
- Not All Sequence Tags Are Created Equal: Designing and Validating Sequence Identification Tags Robust to Indels
- (2012) Brant C. Faircloth et al. PLoS One
- Groundtruthing Next-Gen Sequencing for Microbial Ecology–Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing
- (2012) Charles K. Lee et al. PLoS One
- Use of Four Next-Generation Sequencing Platforms to Determine HIV-1 Coreceptor Tropism
- (2012) John Archer et al. PLoS One
- High-throughput sequencing of ancient plant and mammal DNA preserved in herbivore middens
- (2012) Dáithí C. Murray et al. QUATERNARY SCIENCE REVIEWS
- Deep Sequencing of Plant and Animal DNA Contained within Traditional Chinese Medicines Reveals Legality Issues and Health Safety Concerns
- (2012) Megan L. Coghlan et al. PLoS Genetics
- Strategy for Modular Tagged High-Throughput Amplicon Sequencing
- (2011) Daniel Aguirre de Cárcer et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- UCHIME improves sensitivity and speed of chimera detection
- (2011) Robert C. Edgar et al. BIOINFORMATICS
- Removing Noise From Pyrosequenced Amplicons
- (2011) Christopher Quince et al. BMC BIOINFORMATICS
- Advancing analytical algorithms and pipelines for billions of microbial sequences
- (2011) Antonio Gonzalez et al. CURRENT OPINION IN BIOTECHNOLOGY
- Targeted Amplicon Sequencing (TAS): A Scalable Next-Gen Approach to Multilocus, Multitaxa Phylogenetics
- (2011) Seth M. Bybee et al. Genome Biology and Evolution
- MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods
- (2011) K. Tamura et al. MOLECULAR BIOLOGY AND EVOLUTION
- Meta-barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity
- (2011) KENNETH ANDERSEN et al. MOLECULAR ECOLOGY
- Monitoring endangered freshwater biodiversity using environmental DNA
- (2011) PHILIP FRANCIS THOMSEN et al. MOLECULAR ECOLOGY
- Who is eating what: diet assessment using next generation sequencing
- (2011) FRANCOIS POMPANON et al. MOLECULAR ECOLOGY
- Molecular Diet Analysis of Two African Free-Tailed Bats (Molossidae) Using High Throughput Sequencing
- (2011) Kristine Bohmann et al. PLoS One
- Large Scale Library Generation for High Throughput Sequencing
- (2011) Erik Borgström et al. PLoS One
- DNA-Based Faecal Dietary Analysis: A Comparison of qPCR and High Throughput Sequencing Approaches
- (2011) Dáithí C. Murray et al. PLoS One
- Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies
- (2011) Patrick D. Schloss et al. PLoS One
- High-throughput sequencing offers insight into mechanisms of resource partitioning in cryptic bat species
- (2011) Orly Razgour et al. Ecology and Evolution
- Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
- (2011) Daniel Aird et al. GENOME BIOLOGY
- High-throughput DNA sequencing - concepts and limitations
- (2010) Martin Kircher et al. BIOESSAYS
- Search and clustering orders of magnitude faster than BLAST
- (2010) Robert C. Edgar BIOINFORMATICS
- An In silico approach for the evaluation of DNA barcodes
- (2010) Gentile Ficetola et al. BMC GENOMICS
- Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out?
- (2010) Bruce E. Deagle et al. CONSERVATION GENETICS
- Applications of next generation sequencing in molecular ecology of non-model organisms
- (2010) R Ekblom et al. HEREDITY
- Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate
- (2010) J. H. SØNSTEBØ et al. Molecular Ecology Resources
- QIIME allows analysis of high-throughput community sequencing data
- (2010) J Gregory Caporaso et al. NATURE METHODS
- Increased Throughput by Parallelization of Library Preparation for Massive Sequencing
- (2010) Sverker Lundin et al. PLoS One
- Forensic identification using skin bacterial communities
- (2010) N. Fierer et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
- (2010) J. G. Caporaso et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
- (2010) Jeremy Goecks et al. GENOME BIOLOGY
- 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 MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments
- (2009) S. A. Bustin et al. CLINICAL CHEMISTRY
- Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data
- (2009) Micah Hamady et al. ISME Journal
- Species detection using environmental DNA from water samples
- (2008) G. F. Ficetola et al. Biology Letters
- Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes
- (2008) K. E. Varley et al. GENOME RESEARCH
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreDiscover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversation