Evaluation of ddRADseq for reduced representation metagenome sequencing - Concepedia

Concepedia

Publication | Open Access

Evaluation of ddRADseq for reduced representation metagenome sequencing

DOI Full Paper Access

19

Citations

13

References

2017

Year

Michael Y. Liu, Paul Worden, Leigh G. Monahan, Matthew Z. DeMaere, Catherine Burke, Steven P. Djordjevic, Ian G. Charles, Aaron E. Darling

Abstract

Although ddRADseq does introduce some bias in taxonomic representation, the bias is likely to be small relative to DNA extraction bias. ddRADseq appears feasible and could have value as a tool for metagenome-wide association studies.

References

	Year	Citations
Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species Brant K. Peterson, Jesse N. Weber, Emily H. Kay, PLoS ONE Double Digest RadseqEngineeringGeneticsKeystone TechnologyMolecular Genetics	2012	3.7K
Metagenomic microbial community profiling using unique clade-specific marker genes Nicola Segata, Levi Waldron, Annalisa Ballarini, Nature Methods Microbial DiversityMetagenomic Microbial CommunityMolecular EcologyMicrobial EcologyEnvironmental Microbiology	2012	1.8K
Counting absolute numbers of molecules using unique molecular identifiers Teemu Kivioja, Anna Vähärautio, Kasper Karlsson, Nature Methods Molecular CharacterizationAbsolute NumbersComputational BiologyMolecular BiologyMolecular Computing	2011	1.1K
Quantification of Bias Related to the Extraction of DNA Directly from Soils Åsa Frostegård, Sophie Courtois, Vincent Ramisse, Applied and Environmental Microbiology EngineeringGeneticsDna AnalysisGenomicsMolecular Ecology	1999	539
Breaking RAD: an evaluation of the utility of restriction site‐associated DNA sequencing for genome scans of adaptation David B. Lowry, Sean Hoban, Joanna L. Kelley, Molecular Ecology Resources Comparative GenomicsGeneticsAdaptive DivergenceMolecular GeneticsGenomics	2016	466
<scp>RAD</scp>seq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling Brian Arnold, Russell Corbett‐Detig, Daniel L. Hartl, Molecular Ecology	2013	393
Proportionality: A Valid Alternative to Correlation for Relative Data David Lovell, Vera Pawlowsky‐Glahn, Juan José Egozcue, PLoS Computational Biology	2015	305
Metagenomic Sequencing of an In Vitro-Simulated Microbial Community Jenna Morgan, Aaron E. Darling, Jonathan A. Eisen PLoS ONE	2010	246
Demystifying the <scp>RAD</scp> fad Jonathan B. Puritz, Mikhail V. Matz, Robert J. Toonen, Molecular Ecology PhylogeneticsMolecular EcologyInformation SecurityGeneticsEvolutionary Biology	2014	222
Amplification Biases and Consistent Recovery of Loci in a Double-Digest RAD-seq Protocol Jeffrey M. DaCosta, Michael D. Sorenson PLoS ONE	2014	194

Page 1