Bioinformatics

Primary data processing transforms the raw data generated by the sequencing instruments into quality-scored nucleotide sequences (FASTQ format), a requirement for further processing of the data. Additionally, a QC report and checksum files to verify the file integrity of transferred data are generated. This step is an integral part when the sequencing service of the NGS platform at HMGU is used.

Currently primary processing pipelines are available for short read (Illumina) and long read (ONT) sequencing data.

User fees & service usage: Included in sequencing service of NGS platform.

We offer basic processing of single cell and bulk sequencing data for different platforms and technologies including re-processing of published/public datasets. The computational pipelines perform all necessary steps (e.g. alignment, peak calling, feature counting etc.) required for tertiary analyses and generate a QC report. Please see Computational Pipelines for details.

User fees: Per project depending on the number of samples processed.

Customized analysis is tailored to an individual project and can only be done in close collaboration with the customer. At the beginning of each custom analysis we will schedule a mandatory consultation session to discuss the project in detail as well as possible analysis strategies, milestones and expected results. After accepting the written agreement and provision of a valid payment source we will schedule the work. Customers can expect updates in interim meetings and will  also obtain interim reports and a final report with the results. Upon completion of the project the users will receive all data (pipelines, processed data, analysis code) that were generated for the project.

User fees: Scope and costs will be defined in the proposal and listed in an offer which needs to be accepted by the user.

Together with our colleagues from CF Statistical Consulting we regularly run a Data Analysis cafe.  In these sessions we offer consulting e.g around experimental design (prior to start of a project), analysis and computational implementation questions with our users. For more regular consultation we offer Mentoring (see Mentoring tab).

This is an extension of a single consultation meeting for those that need more regular supervision while doing the analysis themselves. A platform staff member meets regularly (e.g. once a week for 1h) for with the user. A short proposal will be created with the contents of the mentoring.

User fees:Initial consulting (1h) is free for HMGU members, afterwards billed hourly.

Helholtz Munich scientist wishing more in depth learning in bioinformatics and NGS-analysis will be embedded into the Bioinformatics team for a limited time (e.g. 3-6 months). Scientists will obtain continuous support from core team members for their project, but will also contribute to other projects in the platform. Prerequisits for the service are basic skills in R, Linux-opeatring systems (+ Bash-Scripting) und ideally Python.

User fee: monthly rate, please contact us for more detail.

Please note: This service can only be made available when core workload allows.

Our mission is to provide state-of-the-art transferrable, reusable and reproducible bioinformatics analysis pipelines for various next generation sequencing (NGS) applications. The platform wants to always keep up and offer service for the latest research developments. Therefore, we collaborate with PhD students and Postdocs who work on genomics projects and develop new computational pipelines and methods. Researchers profit from the platform's knowledge base and learn best practices on how to develop reusable and transferable workflows. Once developed, the workflows are then offered by the platform as a service to its user base.

User fees and service usage: free for HMGU members, please contact us for capacity and details.

Galaxy pipelines

FFor users with no prior experience in bioinformatics and just starting with the analysis of NGS data we recommend taking our courses where we provide basic and advanced training (see Training Courses). Our courses will train you on how to use computational pipelines using Galaxy or Jupyter Notebooks.

Advanced computational pipelines

For the following NGS technologies, computational pipelines were established and are available for platform users and projects. These pipelines are developed using workflow frameworks such as Nextflow [1] or Snakemake [2] and are executed on the compute cluster. The usage is best suited for trained users with bioinformatic background and knowledge of Linux and command line usage.

We offer the processing of your data with the computational pipelines through our Platform services that can be booked via iLabs (Secondary data processing).

Further information for HMGU users regarding the usage of the pipelines is available from here.

Available computational pipelines:

Bulk sequencing

    - RNA-Seq (nf-core) & miRNA-Seq

    - Assembly and identification or Immunoglobulins from RNA-Seq data (igfinder)

    - ChIP-Seq (ChIP-seq, cutandrun, nf-core)

    - ATAC-Seq (nf-core)

    - WGS variant calling (Sarek, nf-core)  

    - Methyl-Seq (nf-core)  

    - Crispr-Seq (nf-core) 

Single cell sequencing

    - 10x-RNA-Seq (standard, multi)  

    - 10x-ATAC-Seq  

    - 10x-Visum (Spatial Transcriptomics)  

    - 10x-VDJ (Immune Profiling)  

    - 10x-Feature-Barcoding  

    - 10x-Multiome (ATAC-seq + RNA-Seq)  

    - Smart-Seq  

    - Single cell variant calling and genomic demultiplexing (vireo, monopogen)  

    - Split-Seq (Parsebio) 

Long read sequencing

    - scnanoseq (nf-core) 

Illumina Genotyping Arrays

    - Karyotyping pipeline

References

[1] https://www.nextflow.io
[2] https://snakemake.readthedocs.io/en/stable/