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SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments

David B Burdick*, Chris C Cavnor, Jeremy Handcock, Sarah Killcoyne, Jake Lin, Bruz Marzolf, Stephen A Ramsey, Hector Rovira, Ryan Bressler, Ilya Shmulevich and John Boyle

Author Affiliations

Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA

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BMC Bioinformatics 2010, 11:377  doi:10.1186/1471-2105-11-377

Published: 14 July 2010

Abstract

Background

High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires.

Results

Existing software solutions provide static and well-established algorithms in a restrictive package. However as high throughput sequencing is a rapidly evolving field, such static approaches lack the ability to readily adopt the latest advances and techniques which are often required by researchers. We have used a loosely coupled, service-oriented infrastructure to develop SeqAdapt. This system streamlines data management and allows for rapid integration of novel algorithms. Our approach also allows computational biologists to focus on developing and applying new methods instead of writing boilerplate infrastructure code.

Conclusion

The system is based around the Addama service architecture and is available at our website as a demonstration web application, an installable single download and as a collection of individual customizable services.