Theses and Dissertations Collection

HTStream is a suite of applications developed in C++11 that helps users streamline analysis of High Throughput Sequencing data. Current analysis "pipelines" are often rigid and difficult to use, whereas HTStream was designed to enhance the users' experience. To do this, we introduces a new tab delimited FASTQ format which which allows users to combine applications with the use of simple Linux pipes. This ability creates a paradigm shift toward analysis. This usage of pipes reduces storage space, execution time, since no intermediate files are created. Additionally, this reduction in time and reduction in difficulty while doing analysis creates ease of use for end users while concurrently giving them more power, since integration of de facto Linux tools is straightforward.