Hello, and welcome to the whole Enchilada Suite! This is a bioinformatic pipeline created to help streamline genome-wide association studies for those using the sunflower association mapping population first described by Mandel et al (2011; http://www.theburkelab.org/reprints/TAG2011.pdf) and more expanded upon by Mandel et al (2013; http://www.theburkelab.org/reprints/PLoSGenet2013.pdf).
The Enchilada Suite is designed to work as a series of self-contained sequential modules: (1) Burrito, (2) SALSA, and (3) GUAC, which are defined in more detail within their own README files. The downloadable folder is pre-partitioned into the main folders (A) Enchilada Suite, (B) Outputs, (C) Phenos, and (D) Scripts. Enchilada Suite houses each module as a separate folder, each of which contains all necessary folders and programs to run. Outputs is the location where the various plots and tables generated by the pipeline are placed. Phenos is the folder where least-square mean values of all measured traits are housed (see Burrito README). Finally, Scripts is a folder that houses the scripts used in this pipeline.
In the main Enchilada Suite folder, you have to type the command: perl EnchiladaSuite.pl Environments.list Triats.list
This will run all modules sequentially with default parameters (these can be changed, see individual READMEs), for all environments and all traits. Please note that this script can be run for 1 to 5 environments, and an unlimited number of traits, keeping in mind that they are uniquely named.
This pipeline was created by Rishi R. Masalia, University of Georgia, Burke Lab. Burrito was created in collaboration with Sariel Hubner, University of British Columbia. Programs used in this pipeline: EMMAX (Kang, 2010), LDselect.pl (Carlson et al, 2004), PLINKv1.9 (Purcell and Chang, 2017), as well as R packages: data.table (Dowle, 2017), ggplot2 (Wickham, 2009), lme4 (Bates et al, 2015), qqman (Turner, 2014), RColorBrewer (Neuwirth, 2005), SNPRelate (Zheng et al, 2012).