• The workshop will be given in the Faculty of Education Science and Psychology, at the Campus de Teatinos of the University of Malaga (Bulevar Louis Pasteur 25, Málaga). Some volunteers will wait for organizers and attendees at the main entrance of the building, and will guide to the workshop room.
• Level:  Geared toward practicing field biologists with little or no computational experience
• Equipment needed:  Laptop computer
• Maximum capacity: 30 people
• Cost 85 Euros pp

Organizers:

• Isaac Overcast (City College of New York)
• Deren Eaton (Columbia University)

Description:

Over the last 10 years biogeographers have increasingly transitioned from investigating phylogeographic patterns in space and time using datasets composed of one or only a handful of markers to massive datasets containing thousands or tens of thousands of “anonymous” nuclear loci generated using restriction site associated DNA sequencing (RAD-Seq). These larger datasets provide more robust phylogenetic estimates, and can provide additional sources of information such as evidence of historical introgression. The process of organizing and making sense of the vast quantities of reads that come back off a sequencing instrument is non-trivial, and of great consequence. Simple parameter misspecification during the assembly process can have considerable impact on all downstream analysis, potentially influencing the interpretation of the genetic patterns in the data. Prior to the availability of unified assembly tools, these datasets were typically assembled in an ad hoc fashion using scripts developed in-house, leading to wide variability in the quality of assemblies being performed by the community. Additionally, downstream analysis typically involves writing complicated scripts to manage running multiple iterations of statistical inference software, organizing and post-processing the output, and generating publication-ready plots. This proliferation of methods and lack of community standards has two significant consequences:

1. Unnecessary complexity in assembly and analysis workflows increases the potential for introducing errors in the process, which increases the potential for researchers to interpret signals in the data which are essentially meaningless;
2. Because of the extreme contingency of ad hoc scripts developed in-house within labs, these workflows are rarely if ever reused or evaluated by other labs, which is a significant hindrance to reproducibility in science.

In this workshop we will introduce ipyrad, a unified and self-contained RAD-Seq assembly and analysis framework, which emphasizes simplicity, performance, and reproducibility. We will proceed through all the steps necessary to assemble a small simulated RAD-Seq dataset, including demultiplexing reads to samples, cleaning and trimming reads, clustering, basecalling, and generating multiple output types for downstream analysis. We will introduce both the command line interface, as this is typically used in high performance computing settings, and the ipython notebook API, which allows researchers to generate documented and easily reproducible workflows. Additionally, we will introduce the ipyrad ‘analysis’ API which provides a powerful, simple, and reproducible interface to several widely used methods for inferring phylogenetic relationships, population structure, and admixture. The analysis API leverages the massive parallelization provided by the ipyrad backend, manages organization of intermediate files, and provides a simple interface for generating publication-ready plots of results.