The Sequence Read Archive is the world’s largest collection of raw DNA sequencing data and while it provides an adequate online search functionality for interactively finding datasets, downloading them remains unintuitive and technically difficult, especially when downloading a large number of datasets. This project not only simplifies downloading files from the SRA but provides a method to analyze the dataset using read mapping (Bowtie 2). This project also includes tools for many common tasks such as splitting BAM files by organism, graphing coverage and conservation of mapped reads, making heat maps and finding target sites for DNA based technologies; these features will be demonstrated using two phages, crAssphage and a Bacteroides spp. prophage.
