About OTP
As Next-Generation Sequencing (NGS) is a common tool in research and produces huge amount of data, a platform for managing and processing these data is highly required.
The One Touch Pipeline (OTP) was developed with the purpose to organize and process NGS data in an automated, organized and scalable way. OTP also provides a user management interface to control secure data access.
All processing workflows available in OTP are triggered automatically to remove the burden of routine tasks from scientists. The processing steps are stored in the database to allow reproducibility.
Currently, the following pipelines are offered:
| WGS | Exome | ChIP-seq | RNA | WGBS | 10x_scRNA | |
|---|---|---|---|---|---|---|
| Alignment | human mouse |
human mouse |
human mouse |
human mouse |
human mouse |
|
| Cell Ranger count | human mouse |
|||||
| SNV | human | human | ||||
| Indel | human | human | ||||
| SV (Sophia) | human | human | ||||
| CNV (ACESeq) | human | |||||
| runYapsa | human | human |
Meta-information and processing results can be explored in the user interface of OTP. OTP is used for DKFZ in-house projects such as the Heidelberg Center for Personalized Oncology (HIPO) as well as for (inter-)national projects such as the German Network for Translational Cancer Research (DKTK), the German contributions to the International Cancer Genome Consortium (ICGC) and clinical projects like INdividualized Therapy FOr Relapsed Malignancies in Childhood (INFORM) and Molecularly Aided Stratification for Tumor Eradication (MASTER).
In the context of the German Network for Bioinformatics Infrastructure (de.NBI), OTP is provided 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. The medical informatics consortium HiGHmed intends the rollout of OTP within its omics data integration centers (omicsDIC). Within HiGHmed OTP is also being installed at Charité in Berlin.
For further information please refer to our FAQs or 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