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

Abstract

AbSTrACT. Optimizing and monitoring the data flow in highthroughput sequencing facilities is important for data input and output, for tracking the status of results for the users of the facility, and to guarantee a good, high-quality service. In a multi-user system environment with different throughputs, 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-capillary 3730 DNA Sequence Analyzer (Applied Biosystems) and supporting 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. The pipeline (named ChromaPipe for Chromatogram Pipeline) is available for download by the scientific community at the url http://bioinfo. pdtis.fiocruz.br/ChromaPipe/. The support for assembly is also configured as a web service: http://bioinfo.pdtis.fiocruz.br/Assembly/.

Interferon Regulatory Factor 2 Binding Protein 2 Is a New NFAT1 Partner and Represses Its Transcriptional Activity

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Rapid Identification of Sporothrix Species by T3B Fingerprinting

“…Similarity coefficients were calculated using the Dice algorithm, and cluster analysis was performed by means of the unweighted-pair group method using average linkages (UPGMA). Sequencing of the CAL gene was performed as previously described (17) using the sequencing platform at Fiocruz, Brazil (20). Sequences were edited with Sequencer 4.6 (Genes Codes Corporation), aligned with MEGA 4.0.2 software, and compared with sequences available from NCBI GenBank by BLAST.…”

Genome Sequence of Mycobacterium bovis BCG Moreau, the Brazilian Vaccine Strain against Tuberculosis

“…The sequence was obtained from the shotgun sequencing of approximately 20,640 templates from 2 independent pBluescript libraries (average inserts of 2 kb and a 5-to 10-kb range), yielding over 50,000 reads. Sequencing was performed in an ABI 3730 DNA sequencer (Fiocruz/PDTIS sequencing platform; Applied Biosystems) (14). The reads were assembled using Phrap (http://www.phrap.org/), and gaps were closed by direct sequencing of PCR templates with primers designed using Consed (8).…”