About OTP
As Next-Generation Sequencing (NGS) is a common tool in research, a platform for managing and processing these data is highly required.
The One Touch Pipeline (OTP) handles all digital processing steps from import of raw sequence data via alignment of sequencing reads to identification of genomic events in an automated and scalable way.
OTP covers the field between sequencing unit and bioinformatics expert analysis, providing alignment of reads to a reference genome and mutation calling with all steps book-kept in a database.
Processing
Currently the following pipelines are offered:
| WGS | Exome | ChIP-seq | RNA | WGBS | |
|---|---|---|---|---|---|
| Alignment | human mouse | human mouse | human mouse | human mouse | human mouse |
| SNV | human | human | |||
| InDel | human | human | |||
| SV (Sophia) | human | human | |||
| CNV (ACESeq) | human | ||||
| runYapsa | human | human |
Variants can only be called for tumor-control pairs. We do currently not offer a no-control workflow.
This automation leads to several advantages:
- reduction of human resources required for management of sequenced data
- reduction of time until data can be further analyzed by bioinformatics experts
- executing all operations more reliable and quickly
- storage of all relevant information in a uniform way in one system with secure web access and search capabilities
OTP addresses both fields: information center and work flow management system. For workflow management, several NGS pipelines can be called and easily be adapted and extended according to new requirements. The information center part comprises a database or metadata information and a structured file system.
OTP was used in DKFZ’s in-house projects like the Heidelberg Center for Personalized Oncology (HIPO) as well as to partners in the German Network for Translational Cancer Research (DKTK) and the German contributions to the International Cancer Genome Consortium (ICGC).
In the context of the German Network for Bioinformatics Infrastructure (de.NBI), OTP is widespread to the German bioinformatics community as a service. This distribution of OTP is supported by the BMBF-funded Heidelberg Center for Human Bioinformatics (HD-HuB) within de.NBI.
For further information and consulting please contact odcf-service@dkfz-heidelberg.de.
References
[1] Reisinger, E., Journal of Biotechnology (2017), http://dx.doi.org/10.1016/j.jbiotec.2017.08.006