OTP: An automatized system for managing and processing NGS data

•OTP has processed 20.000 samples to date and contains the data of all German submissions to ICGC and of DKTK.•OTP normally requires no manual intervention for data import, processing and error handling enabling 24/7 operation.•OTP can interact with any job execution framework containing bioinformatic pipelines to integrate new pipelines.•OTP integrates a database containing all information about the sequencing data; from the sample preparation to analyses.•OTP provides structured data storage, user management to ensure data security and an intuitive graphical user interface.

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.