Data handling strategies for high throughput pyrosequencers

Background: New high throughput pyrosequencers such as the 454 Life Sciences GS 20 are capable of massively parallelizing DNA sequencing providing an unprecedented rate of output data as well as potentially reducing costs. However, these new pyrosequencers bear a different error profile and provide shorter reads than those of a more traditional Sanger sequencer. These facts pose new challenges regarding how the data are handled and analyzed, in addition, the steep increase in the sequencers throughput calls for much computation power at a low cost. Results: To address these challenges, we created an automated multi-step computation pipeline integrated with a database storage system. This allowed us to store, handle, index and search (1) the output data from the GS20 sequencer (2) analysis projects, possibly multiple on every dataset (3) final results of analysis computations (4) intermediate results of computations (these allow hand-made comparisons and hence further searches by the b...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Gabriele A. Trombetti, Raoul J. P. Bonnal, Ermanno Rizzi, Gianluca De Bellis, Luciano Milanesi
• Keywords: 454 Life Sciences, BMCBI 2007, Computation, Output Data