GenOO : a programming framework for High Throughput Sequencing analysis

Abstract

Background: High throughput sequencing (HTS) has become one of the primary experimental tools used to extract genomic information from biological samples. Bioinformatics tools are continuously being developed for the analysis of HTS data. Beyond some well-defined core analyses, such as quality control or genomic alignment, the consistent development of custom tools and the representation of sequencing data in organized computational structures and entities remains a challenging effort for bioinformaticians. Results: In this work, we present GenOO [jee-noo], an open-source; object-oriented (OO) Perl framework specifically developed for the design and implementation of HTS analysis tools. GenOO models biological entities such as genes and transcripts as Perl objects, and includes relevant modules, attributes and methods that allow for the manipulation of high throughput sequencing data. GenOO integrates these elements in a simple and transparent way which allows for the creation of complex analysis pipelines minimizing the overhead for the researcher. GenOO has been designed with flexibility in mind, and has an easily extendable modular structure with minimal requirements for external tools and libraries. As an example of the framework’s capabilities and usability, we present a short and simple walkthrough of a custom use case in HTS analysis. Conclusions: GenOO is a tool of high software quality which can be efficiently used for advanced HTS analyses. It has been used to develop several custom analysis tools, leading to a number of published works. Using GenOO as a core development module can greatly benefit users, by reducing the overhead and complexity of managing HTS data and biological entities at hand.