Breseq: coding a tool for mutation identification in next-generation microbial genome sequencing data

This project is closed.

This project aims to continue development of the breseq software and related open-source code for predicting mutations from microbial genome re-sequencing data. The tool supports research in the Barrick lab studying mutations that occur during evolution experiments with bacteria in several contexts.

We are looking for individuals with some programming knowledge to work as part of a team on this complex software project that has sub-projects accessible to coders with many different levels of experience. These opportunities range from developing and testing improved algorithms for predicting certain kinds of mutations to creating new ways of visualizing results and integrating them in an evolutionary framework.

Additional information about breseq is available here:

This is an excellent opportunity for computational biology or computer science majors to gain hands-on experience tackling bioinformatics challenges, dealing with genomic data, and using the Texas Advanced Computing Center. Related computational projects simulating microbial and molecular evolution in different contexts are also possible. Opportunities also exist for students with a computational background to try out some "wet-lab" microbiology experiments related to this work depending on their interests.


Python, C++, or Perl programming experience required. For various projects, familiarity with Linux, R, Biopython, and HTML would be helpful.


We are looking for applicants able to work independently for 10+ hours per week on a defined project for at least two semesters. Compensation (including full-time hours during the Summer) as an undergraduate research assistant is available for outstanding and dedicated individuals after they have volunteered for at least one semester.

Typical Time Commitment
Desired Length of Commitment


The Office of Undergraduate Research recommends that you attend an info session or advising before contacting faculty members or project contacts about research opportunities. We'll cover the steps to get involved, tips for contacting faculty, funding possibilities, and options for course credit. Once you have attended an Office of Undergraduate Research info session or spoken to an advisor, you can use the "Who to contact" details for this project to get in touch with the project leader and express your interest in getting involved.

Have you tried contacting professors and need more help? Schedule an appointment for additional support.