| Abstract Detail
Conference Wide Eaton, Deren [1]. Assembly and analysis of genomic RADseq data using ipyrad. Restriction-site associated DNA sequencing (RADseq) and related methods (e.g., ddRAD, GBS) provide a simple and fast way to sample sequence data from thousands of genomic regions across many sampled individuals. The goal of this workshop is to introduce participants to the software ipyrad, which can be used to assemble and analyze RADseq data sets. We will begin with an introduction to what RADseq is, how the data are generated, and what the raw data look like. We will then learn the general workflow of ipyrad, and use it to assemble empirical test data sets. This will be followed by an introduction to more advanced Python scripting using the ipyrad API. We will end with methods for visualizing assembled data and analyzing results with population genetic summary statistics and tests for introgression. This workshop will be taught through the use of Jupyter Notebooks, with a goal of introducing participants to how this tool can be used to create reproducible published bioinformatic workflows. No previous coding experience is required. Attendees will need a laptop running either mac or linux.
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1 - Yale University, Ecology and Evolutionary Biology, 21 Sachem st., Environmental Science Center 366, New Haven, CT, 06511, USA
Keywords:
Genomics
Bioinformatics
Python
RADseq
Reproducibility.
Presentation Type: Workshop
Session: WS07, Assembly and analysis of genomic RADseq data using ipyrad
Location: 106/Savannah International Trade and Convention Center
Date: Sunday, July 31st, 2016
Time: 8:00 AM
Number: WS07001
Abstract ID:19
Candidate for Awards:None |
