This is a (currently incomplete) reformatting of the DrosEU pipeline available on GitHub and described in this paper. The goal is to perform similar analysis methods in a more automated manner on WSU's Kamiak cluster. The initial wrapper implementation will be in R, calling external tools as necessary.

The config.R script holds all user-definable analysis options and parameters.

The full analysis is separated into several scripts to allow for breakpoints after computationally intensive procedures.

The s1.sequence.processing.R script requires the config.R configuration file. It reads raw FASTQ files, performs basic QC, and maps the quality reads to a reference genome using BWA. The final output will be both QC summary reports as well as sorted BAM files.

The s2.decontamination.R script requires the config.R configuration file and the output files from s1.sequence.processing.R. It removes any potential D. simulans contamination.

The s3.snp.analysis.R script requires the config.R configuration file and the output files from s1.sequence.processing.R. It generates the Pileup file combining all study samples and calls SNPs. It then filters SNPs based on several characteristics. Finally, the script annotates any identified SNPs.

The s4.additional.analyses.R script requires the config.R configuration file and the output files from s1.sequence.processing.R and s3.snp.analysis.R. It performs several analyses including calculation of Watterson's Theta, Tajima's D, Tajima's pi, pairwise Fst, isolation by distance, and other values.

The s5.generate.reports.R script requires the config.R configuration file and the output from the previous pipeline steps. It generates a summary of the pipeline results, including QC metrics, a description of the analyses performed with parameter values, and relevant figures and tables.