Service
Bioinformatics Facility
Services
- Galaxy Server: for 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: we operate a state-of-the-art high performance storage unit that 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 webservices like Galaxy and R-Studio, provide centralised home directories and logins, serve as data capture for the sequencing machines or are simply compute servers to run analysis on. Two of these compute servers (minimus, maximus) are also available to any institute member. 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 on the 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 analysis
snakeQuest
A web-based query for snakePipes analyses
Parkour LIMS
high-quality sample preparation in NGS
Training
- Galaxy course: 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 course: Find the course material online.
- Linux course: Materials from our Linux course are still available online.