Tag Archives: ddRADseq

At the University of Florida, SageELF Delivers Better Sizing for ddRAD-seq and Long-Read Pipelines

Clients of the NextGen DNA Sequencing core at the University of Florida in Gainesville rely on Scientific Director David Moraga Amador to find and validate the best technologies for their projects. In addition to bringing in the best sequencers, that … more »

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RADcap: sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data

August 2016 Authors: Hoffberg SL, Kieran TJ, Catchen JM, Devault A, Faircloth BC, Mauricio R, Glenn TC Info: In this methods paper, scientists combine double-digest RAD-seq with capture technology to reduce costs and increase efficiency. The protocol, which was validated … more »

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PELE-seq Increases SNP Calling Accuracy by Reducing Sequencing Errors

Scientists at the University of Oregon have published a new method to detect PCR and sequencing errors that should help other researchers track rare SNPs with greater accuracy. PELE-seq, which gets our vote for best new protocol name, can be … more »

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Urban Mice: NYC Study Sheds Light on Population Diversity and Changes

They may make subway riders shudder, but New York City mice are the stars of a cool new paper outlining their evolutionary history during a rapid period of urbanization. Scientists from the City University of New York used ddRAD-seq to … more »

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Building on a RAD Idea

It’s been a few years since the Hoekstra lab at Harvard first published its double-digest RAD-seq protocol. Since then, the approach has been rapidly adopted by the community for massively parallel genotyping, particularly of non-model organisms, and has been the … more »

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Urbanization shapes the demographic history of a native rodent (the white-footed mouse, Peromyscus leucopus) in New York City

April 2016 Authors: Stephen E. Harris, Alexander T. Xue, Diego Alvarado-Serrano, Joel T. Boehm, Tyler Joseph, Michael J. Hickerson, Jason Munshi-South Info: Researchers at the City University of New York studied populations of white-footed mice in New York City and … more »

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Patterns of genome-wide variation in Glossina fuscipes fuscipes tsetse flies from Uganda

April 2016 Authors: Gloria-Soria A, Dunn WA, Telleria EL, Evans BR, Okedi L, Echodu R, Warren WC, Montague MJ, Aksoy S, Caccone A Info: Researchers used ddRAD-seq to develop a panel of SNPs for use in population genomics or genome-wide … more »

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Harnessing the power of RADseq for ecological and evolutionary genomics

January 2016 Authors: Kimberly R. Andrews, Jeffrey M. Good, Michael R. Miller, Gordon Luikart and Paul A. Hohenlohe Info: In this protocol review, scientists examine several approaches to restriction site-associated DNA sequencing and present their findings on how to choose … more »

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EpiRADseq: scalable analysis of genomewide patterns of methylation using next-generation sequencing

August 2015 Authors: Drew R. Schield, Matthew R. Walsh, Daren C. Card, Audra L. Andrew, Richard H. Adams and Todd A. Castoe Info: University of Texas researchers present a new method for quantifying methylation patterns across whole genomes at low … more »

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Limitations of Climatic Data for Inferring Species Boundaries: Insights from Speckled Rattlesnakes

June 2015 Authors: Jesse M. Meik, Jeffrey W. Streicher, A. Michelle Lawing, Oscar Flores-Villela, and Matthew K. Fujita Info: In this paper, scientists in Texas and Mexico challenge conventional climate-based species boundaries in the speckled rattlesnake, using genomic and other … more »

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