Group items tagged

A tool for visualizing abnormal read pairs (i.e. too far apart, forward-forward or reverse-reverse). One of the ways to identify structural variation in a genome is to look at mapping of a read-pair library on a reference genome. Any read-pair (i.e. the ends of the same clone) normally maps in a forward-reverse orientation at a distance from each other that corresponds to the insert size of the clone library. Structural variation between the reference genome used for mapping and the genome used to create the clone library will cause the reads to map in the wrong orientation (i.e. forward-forward or reverse-reverse; indicating an inversion) or at too large or too small a distance (indicating an insertion or deletion in the sample, respectively). pARP basically displays raw read pair mapping data and does not make any assumptions on models as might be required when doing a statistical analysis of the same data. By showing a birds' eye view it helps in interpreting what structural variations are present.

The Open Bioinformatics Foundation or O|B|F is a non profit, volunteer run organization focused on supporting open source programming in bioinformatics. The foundation grew out of the volunteer projects BioPerl, BioJava and BioPython and was formally incorporated in order to handle our modest requirements of hardware ownership, domain name management and funding for conferences and workshops.The Foundation does not participate directly in the development or structure of the open source work, but as the members of the foundation are drawn from the member projects, there is clear commonality of direction and purpose. Occasionally the O|B|F directors may make announcements about our direction or purpose (a recent one was on the licensing of academic software) when the board feels there is a need to clarify matters, but in general we prefer to remain simply the administrative support organization for our member projects. Our main activities are: * Underwriting and supporting the BOSC conferences * Organizing and supporting developer-centric "hackathon" events * Managing our servers, colocation facilities, bank account & other assets We are incorporated in the state of Delaware, USA as a not-for-profit company.