NGS Services

The Biomedical Sequencing Facility offers a broad range of NGS-related services, including library preparation (genome, epigenome, transcriptome, single-cell sequencing, etc.), sequencing of custom libraries on Illumina NovaSeq, HiSeq 3000, MiSeq and Oxford Nanopore platforms, and bioinformatic data processing. A detailed list of prices and services is available on request.

NGS Advice and Consulting

We are happy to advise and contribute our expertise regarding study design (e.g. how many replicates), protocol selection, bioinformatic analysis etc. We can also provide quotes for grant applications.

Library Preparation

The BSF offers library preparation for whole genome, targeted genome, transcriptome, epigenome and single-cell NGS projects. For large-scale NGS projects the BSF is equipped with a pre- and post PCR high-throughput liquid handling system as well as with a 10x Genomics Single Cell Controller for ultra high-throughput single-cell transcriptomics.


Genome Library Preparation

 - Whole genome

 - Comprehensive human exome


Transcriptome Library Preparation

- Stranded mRNA-seq (poly-A enrichment)

- Low-input RNA-seq

- Transcription fingerprinting 3' RNA-seq protocol


Epigenome Library Preparation

- Reduced representation bisulfite sequencing (RRBS)

- Whole genome bisulfite sequencing

- High-throughput chromatin profiling (ATAC-seq)

- ChIP-seq


Single-cell Library Preparation

- Single-cell RNA-seq (Smart-Seq)

- Massive-scale, low-coverage single-cell RNA-seq (10x Genomics)


Custom Library Preparation

- please inquire


Please find the sequencing recommendations for each protocol in the Materials section

Next Generation Sequencing

For genomic research, the BSF uses the latest Illumina NGS technology, including the NovaSeq 6000 for highest throughput and cost efficiency, the HiSeq 3000 for high throughput, and the MiSeq for hotspot gene panels and other small-scale applications as well as Oxford Nanopore Sequencing technology for long read applications.


HiSeq 3000 Sequencing

High throughput, flexibility, cost-efficiency for a broad range of applications


- 1 x 50 bp (single-read)


estimated reads passing filter per lane: 312,5 million


NovaSeq 6000 Sequencing

Highest throughput and cost effectiveness for large-scale projects


- 1 x 35 bp (single-read, S4 flow cell)

- 2 x 50 bp (paired-end, SP, S1, and S2 flow cell)

- 2 x 100 bp (paired-end, SP, S1, S2 and S4 flow cell)

- 2 x150 bp (paired-end, SP, S1, S2 and S4 flow cell)

- 2 x 250 bp (paired-end, SP flow cell)


estimated reads passing filter per flow cell: 800 million (SP), 1.6 billion (S1), 4.1 billion (S2) and 10 billion (S4)


MiSeq Sequencing

Flexibility and cost effectiveness for small-scale assays


- 1 x 50 bp (single-read, v2)

- 2 x 75 bp (paired-end, v3)

- 2 x 150 bp (paired-end, v2 nano, v2 micro and v2)

- 2 x 250 bp (paired-end, v2 nano and v2)

- 2 x 300 bp (paired-end, v3)

estimated reads passing filter per flow cell: 1 million (v2 nano), 4 million (v2 micro), 15 million (v2) and 25 million (v3)



Other Sequencing Platforms

Long reads


- Oxford Nanopore (MinION and PromethION)


Custom Sequencing

- please inquire


Please find an overview of the specifications of the sequencing systems in the Material section


The BSF preprocesses sequencing data and offers a basic bioinformatic analysis.  Furthermore the BSF is supported by a powerful scientific computing cluster that is upgraded annually to keep pace with steeply increasing amounts of data generation (current status: >100 CPUs, >1,000 cores, >10 TB memory, >1,000 TB storage).




- Data preprocessing (demultiplexing and transfer of unaligned BAM file)

- Basic bioinformatic analysis (alignment and genome browser visualization of BAM file)

- Additional bioinformatic analysis (e.g. differential expression or genotype calling)

- Long-term data storage in accordance with project requirements

- Assistence with publication-related data sharing requirements (e.g. GEO submission)