Next-gen sequencing: data acquisition, comparative genomics, design and analysis for population genetics, systematics and development

PI(s): Brian O'Connor (University of North Carolina-Chapel Hill)
Willam Cresko (University of Oregon)
Christine Elsik (Georgetown University)
James Noonan (Yale University)
Jeffrey Townsend (Yale University)
Jennifer Taylor (Australian National University)
Greg Wray (Duke University)
Konrad Paszkiewicz (University of Exeter)
Alexie Papanicolaou (CSIRO)
Start Date: 15-Aug-2011
End Date: 29-Aug-2011
Keywords: software, comparative methods, population genetics, systematics

This 2-week course will provide the computational training required for workers in this diverse field and is aimed in particular at second-year graduate students, research fellows and faculty crossing the field into genomics. The course will be embedded within an array of biological questions but it will be focused around specific technical questions such as i) generation of gene-models from related reference genomes or from NGS transcriptomes, ii) variant calling and alternative splicing detection, iii) analyzing differential expression, iv) mapping of eQTL data, v) genome-wide tests for selection, vi) generation and use of genome-wide SNP markers, vii) analysis of metagenomic data, and viii) phylogeny reconstruction from NGS. Instructors from diverse backgrounds will lead students through lectures and practicals designed to give students concrete experience working with a diverse set of analysis tools and techniques. At the end of this course, participants will i) have a concrete understanding of the general power and limitations of NGS, ii) understand which tools should be used and why, and iii) be able to address a biological question of interest using the raw data from the sequencing machine. An added advantage of attending this course will be the creation of a community of researchers familiar with an interoperable set of tools, providing continued support and the potential for collaboration into the future.

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