期刊
JOURNAL OF BIOTECHNOLOGY
卷 261, 期 -, 页码 53-62出版社
ELSEVIER
DOI: 10.1016/j.jbiotec.2017.08.006
关键词
Next-generation sequencing; Data management; Data processing; Automation; User interface; Standardization
资金
- German Federal Ministry of Education and Research (BMBF) project LungSys [0315415A]
- German Federal Ministry of Education and Research (BMBF) project ICGC PedBrainTumor [01KU1201A]
- German Federal Ministry of Education and Research (BMBF) project CancerSys LungSysII [0316042A]
- German Federal Ministry of Education and Research (BMBF) project CancerSys MYCeNET [0316076B]
- German Federal Ministry of Education and Research (BMBF) project ICGC:The Genomes of Early Onset Prostate Cancers [01KU1001A]
- German Federal Ministry of Education and Research (BMBF) project ICGC Malignant Lymphoma [01KU1002B]
- German Federal Ministry of Education and Research (BMBF) project e:BIO: ImmunoQuant [0316170A]
- German Federal Ministry of Education and Research (BMBF) project e:MED - PANC-STRAT [01ZX1305A]
- German Federal Ministry of Education and Research (BMBF) project Deutsches Epigenom-Projekt DEEP [01KU1216B]
- German Cancer Aid ICGC PedBrainTumor [109252]
- Initiative and Networking Fund of the Helmholtz Association within the Helmholtz Alliance on Systems Biology
- Heidelberg Center for Personalized Oncology (DKFZ-HIPO)
- BMBF within the German Network for Bioinformatics Infrastructure (de.NBI) [031A537A, 031A537C]
The One Touch Pipeline (OTP) is an automation platform managing Next-Generation Sequencing (NGS) data and calling bioinformatic pipelines for processing these data. OTP handles the complete digital process from import of raw sequence data via alignment of sequencing reads to identify genomic events in an automated and scalable way. Three major goals are pursued: firstly, reduction of human resources required for data management by introducing automated processes. Secondly, reduction of time until the sequences can be analyzed by bioinformatic experts, by executing all operations more reliably and quickly. Thirdly, storing all information in one system with secure web access and search capabilities. From software architecture perspective, OTP is both information center and workflow management system. As a workflow management system, OTP call several NGS pipelines that can easily be adapted and extended according to new requirements. As an information center, it comprises a database for metadata information as well as a structured file system. Based on complete and consistent information, data management and bioinformatic pipelines within OTP are executed automatically with all steps book-kept in a database.
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