ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility

Otto, T.D. , Vasconcellos, E.A., Gomes, L.H.F., Moreira, A.S., Degrave, W.M., Mendonca-Lima, L. and Alves-Ferreira, M. (2008) ChromaPipe: a pipeline for analysis, quality control and management for a DNA sequencing facility. Genetics and Molecular Research, 7(3), pp. 861-871. (PMID:18949705)

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Abstract

Optimizing and monitoring the data flow in high-throughput sequencing facilities is important for data input and output, for tracking the status of results for the users of the facility, and to guar-antee a good, high-quality service. In a multi-user system environment with different hroughputs, each user wants to access his/her data easily, track his/her sequencing history, analyze sequences and their quality, and apply some basic post-sequencing analysis, without the necessity of installing further software. Recently, Fiocruz established such a core facility as a technological platform”. Infrastructure includes a 48-capil-lary 3730 DNA Sequence Analyzer (Applied Biosystems) and support-ing equipment. The service includes running samples for large-scale users, performing DNA sequencing reactions and runs for medium and small users, and participation in partial or full genome projects. We implemented a workflow that fulfills these requirements for small and high throughput users. Our implementation also includes the monitoring of data for continuous quality improvement (reports by plate, month and user) by the sequencing staff. For the user, different analyses of the chromatograms, such as visualization of good quality regions, as well as processing, such as comparisons or assemblies, are available. So far, 180 users have made use of the service, generating 155,000 sequences, 35% of which were produced for the BCG Moreau-RJ genome project.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Otto, Dr Thomas
Authors: Otto, T.D., Vasconcellos, E.A., Gomes, L.H.F., Moreira, A.S., Degrave, W.M., Mendonca-Lima, L., and Alves-Ferreira, M.
College/School:College of Medical Veterinary and Life Sciences > Institute of Infection Immunity and Inflammation
Journal Name:Genetics and Molecular Research
Publisher:GMR
ISSN:16765680
ISSN (Online):1676-5680

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