Literature DB >> 24495199

Recent novel approaches for population genomics data analysis.

Kimberly R Andrews1, Gordon Luikart.   

Abstract

Next-generation sequencing (NGS) technology is revolutionizing the fields of population genetics, molecular ecology and conservation biology. But it can be challenging for researchers to learn the new and rapidly evolving techniques required to use NGS data. A recent workshop entitled 'Population Genomic Data Analysis' was held to provide training in conceptual and practical aspects of data production and analysis for population genomics, with an emphasis on NGS data analysis. This workshop brought together 16 instructors who were experts in the field of population genomics and 31 student participants. Instructors provided helpful and often entertaining advice regarding how to choose and use a NGS method for a given research question, and regarding critical aspects of NGS data production and analysis such as library preparation, filtering to remove sequencing errors and outlier loci, and genotype calling. In addition, instructors provided general advice about how to approach population genomics data analysis and how to build a career in science. The overarching messages of the workshop were that NGS data analysis should be approached with a keen understanding of the theoretical models underlying the analyses, and with analyses tailored to each research question and project. When analysed carefully, NGS data provide extremely powerful tools for answering crucial questions in disciplines ranging from evolution and ecology to conservation and agriculture, including questions that could not be answered prior to the development of NGS technology.
© 2014 John Wiley & Sons Ltd.

Entities:  

Keywords:  bioinformatics; computational analyses; genomic course; next-generation sequencing; statistical genetics; workshop

Mesh:

Year:  2014        PMID: 24495199     DOI: 10.1111/mec.12686

Source DB:  PubMed          Journal:  Mol Ecol        ISSN: 0962-1083            Impact factor:   6.185


  29 in total

1.  Transcriptome resources for the white-footed mouse (Peromyscus leucopus): new genomic tools for investigating ecologically divergent urban and rural populations.

Authors:  Stephen E Harris; Rachel J O'Neill; Jason Munshi-South
Journal:  Mol Ecol Resour       Date:  2014-07-16       Impact factor: 7.090

2.  Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results?

Authors:  Tristan Cumer; Charles Pouchon; Frédéric Boyer; Glenn Yannic; Delphine Rioux; Aurélie Bonin; Thibaut Capblancq
Journal:  Mol Genet Genomics       Date:  2021-01-20       Impact factor: 3.291

Review 3.  Evolution and population genomics of the Lyme borreliosis pathogen, Borrelia burgdorferi.

Authors:  Stephanie N Seifert; Camilo E Khatchikian; Wei Zhou; Dustin Brisson
Journal:  Trends Genet       Date:  2015-03-09       Impact factor: 11.639

4.  Detecting the Genomic Signature of Divergent Selection in Presence of Gene Flow.

Authors:  M J Rivas; S Domínguez-García; A Carvajal-Rodríguez
Journal:  Curr Genomics       Date:  2015-06       Impact factor: 2.236

Review 5.  Challenges in analysis and interpretation of microsatellite data for population genetic studies.

Authors:  Alexander I Putman; Ignazio Carbone
Journal:  Ecol Evol       Date:  2014-10-30       Impact factor: 2.912

6.  Recent insertion/deletion (reINDEL) mutations: increasing awareness to boost molecular-based research in ecology and evolution.

Authors:  Birgit C Schlick-Steiner; Wolfgang Arthofer; Karl Moder; Florian M Steiner
Journal:  Ecol Evol       Date:  2014-12-04       Impact factor: 2.912

Review 7.  Genetic anchoring of whole-genome shotgun assemblies.

Authors:  Martin Mascher; Nils Stein
Journal:  Front Genet       Date:  2014-07-07       Impact factor: 4.599

8.  Microsatellite and major histocompatibility complex variation in an endangered rattlesnake, the Eastern Massasauga (Sistrurus catenatus).

Authors:  Collin P Jaeger; Melvin R Duvall; Bradley J Swanson; Christopher A Phillips; Michael J Dreslik; Sarah J Baker; Richard B King
Journal:  Ecol Evol       Date:  2016-05-17       Impact factor: 2.912

9.  Genotyping-by-Sequencing SNP Identification for Crops without a Reference Genome: Using Transcriptome Based Mapping as an Alternative Strategy.

Authors:  Cécile Berthouly-Salazar; Cédric Mariac; Marie Couderc; Juliette Pouzadoux; Jean-Baptiste Floc'h; Yves Vigouroux
Journal:  Front Plant Sci       Date:  2016-06-15       Impact factor: 5.753

10.  Whole genome sequencing in cats, identifies new models for blindness in AIPL1 and somite segmentation in HES7.

Authors:  Leslie A Lyons; Erica K Creighton; Hasan Alhaddad; Holly C Beale; Robert A Grahn; HyungChul Rah; David J Maggs; Christopher R Helps; Barbara Gandolfi
Journal:  BMC Genomics       Date:  2016-03-31       Impact factor: 3.969

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