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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 »
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 »
Posted in Citation
Tagged ddRADseq, genotyping, Illumina, Methods, NextSeq, Pippin Prep, Target Enrichment
Comments Off on RADcap: sequence capture of dual-digest RADseq libraries with identifiable duplicates and reduced missing data
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 »
Posted in Blog
Tagged ddRADseq, genotyping, HiSeq, Illumina, Methods, Pippin Prep
Comments Off on PELE-seq Increases SNP Calling Accuracy by Reducing Sequencing Errors
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 »
Posted in Blog
Tagged ddRADseq, genotyping, HiSeq, Illumina, Pippin Prep
Comments Off on Urban Mice: NYC Study Sheds Light on Population Diversity and Changes
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 »
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 »
Posted in Citation
Tagged ddRADseq, Pippin Prep
Comments Off on Urbanization shapes the demographic history of a native rodent (the white-footed mouse, Peromyscus leucopus) in New York City
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 »
Posted in Citation
Tagged BluePippin, ddRADseq
Comments Off on Patterns of genome-wide variation in Glossina fuscipes fuscipes tsetse flies from Uganda
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 »
Posted in Citation
Tagged ddRADseq, Pippin Prep
Comments Off on Harnessing the power of RADseq for ecological and evolutionary genomics
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 »
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 »
Posted in Citation
Tagged BluePippin, ddRADseq
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