Service
Bioinformatics Facility
Services
- Galaxy Server: Analysis of NGS data, data access, and sharing
- Workbench: Web interface for interactive software environments and reproducible data analysis: R-Studio, Jupyterlab, Shiny
- NGS primary analysis: Quality control and mapping of NGS data
- Data hosting: Our state-of-the-art high-performance storage unit hosts all internal NGS data in a central place and can be accessed through our Linux servers and Galaxy
- High-performance computing: We also operate a range of different servers that run web services like Galaxy and R-Studio, provide centralized home directories and logins, and serve as data capture for the sequencing machines or as compute servers to run analyses on. Two of these compute servers (minimus, maximus) are also available to all Institute members. They run on Linux (CentOS) and knowledge of the command line is required to operate them. All widely used bioinformatics tools are already installed (e.g., samtools, bedtools, bowtie, macs, deepTools).
Contact bioinfo-core@ie-freiburg.mpg.de to get a login and details for access.
Software
deepTools
User-friendly tools for the normalization and visualization of deep-sequencing data
(also available in our Galaxy Server)
HiCExplorer
Process, normalize, analyze, and visualize Hi-C and Chi-C data
snakePipes
Facilitating flexible, scalable, and integrative epigenomic analyses
snakeQuest
A web-based query for snakePipes analyses
Parkour LIMS
High-quality sample preparation in NGS
Training
- Galaxy courses: In cooperation with the University Freiburg, we have developed an extensive training program for NGS analysis. Upcoming courses are announced via Institute email, but there is a growing compendium resource for self-guided online learning: https://training.galaxyproject.org/
- R courses: Course materials are available online.
- Linux courses: Materials from our Linux course are still available online.