One Touch Pipeline (OTP) is an automation platform for processing next generation sequencing (NGS) data. The application provides support in all steps of this process including data registration, storage handling, quality monitoring, alignment of reads to reference genomes and all crucial types of variant calling. OTP has been developed since 2011 by the Data Management and Genomics IT in eilslabs.

From software architecture perspective, OTP is both information center and workflow system. Meta-data files describing sequences are uploaded into the database, involving curating steps and manual interventions in case of ambiguities. Based on complete and consistent information, data management and bioinformatics workflows are executed with all steps book-kept in a database. CPU and I/O intensive jobs are sent to our high performance computing clusters.

The application provides three major benefits to stakeholders: first, the automation process reduces the man-power required for data management. Second, all operations are executed more reliably and faster reducing the time until the sequences can be analyzed by bio-informatics groups. Third, all information is located in one system with secure web access and search capabilities.

The application was implemented using Grails framework in Groovy programming language with web layer in HTML5. The Grails framework provides support for dependency injection from Spring framework and object relational mapping using Hibernate. The authorization is programmed using Spring Security annotations with authentication based on LDAP system. The application is deployed on Apache Tomcat web container and PostgreSQL is used as a database engine. The application is managing data and processes in two separate computing realms with petabyte scale file system and computing cluster operated by job schedulers as SLURM and PBS in each realm.

OTP is partially used for our internal projects, e.g. the three German projects within the International Cancer Genome Consortium (ICGC), DEEP (Deutsches Epigenom Programm), the German contribution to the International Epidemiological Consortium (IHEC).

External German projects are supported in the context of the Heidelberg Center for Human Bioinformatics as part of the German Network for Bioinformatics Infrastructure (de.NBI) supports OTP for de.NBI users. Among others this are the Heidelberger Center for Personalized Oncology (DKFZ-HIPO) and the German Consortium for Translational Cancer Research (DKTK).

Access to OTP

Access OTP via https://otp.dkfz.de/otp/ (registered users only)