Abstract Detail

Conference Wide

Johnson, Matt [1], Chen, Yanni [1], Price, Sherese [1], Bullock, Madison [1], Slimp, Madeline [1], Patel, Nikisha [2].

Analysis of Target Capture Data for Phylogenetics and Population Genetics.

Targeted sequencing has emerged as a cost-efficient method for generating large datasets in phylogenetics. The use of HybSeq to target exons and flanking noncoding regions in plants holds promise to use the same techniques at the species or population level. The availability of target capture probes designed to work with large groups of organisms (i.e. all angiosperms, or all mosses) makes target capture an exciting method for any lab. Data analysis, however, requires careful consideration of tools, many of which were developed to work with model organisms. For example, researchers should consider the possibility that unexpected gene duplication of “single-copy genes” may bias results when working with plant DNA sequences. At the end of this full day workshop, participants will have experience recovering targeted sequences from high-throughput DNA sequencing reads using HybPiper. Participants will work with data using the UNIX command line and will learn techniques for data summary and visualization. Participants will also learn how to use the output of HybPiper to extract flanking non-coding sequences, analyze data for the presence of paralogs, and generate datasets for population genetics and phylogenetics analysis. Participants should bring a laptop; some experience with the UNIX command line is recommended but not required. This workshop is supported in part by NSF-DEB #1753800 to MGJ.

1 - Texas Tech University
2 - University of Connecticut

Keywords:
none specified

Presentation Type: Workshop
Number: W08001
Abstract ID:5
Candidate for Awards:None