Next Gen Sequencing (NGS)


The Genomics Platform is equipped with the NovaSeq 6000 from Illumina.

This highly robust and accurate sequencing platform is based on massively parallel sequencing of million of reads using proprietary reversible terminator-based sequencing chemistry (see method description in Illumina website).

The system enables sequencing of 100 to 250 bases from one end (single read; SR) or both ends (paired-end; PE) of DNA inserts.

Oxford Nanopore Technologies

The Platform is also equipped with the MinION Mk1C of Oxford Nanopore Technologies. This portable device for real-time DNA and RNA sequencing generates ultra-long reads (longest > 4 Mb) while keeping bases modification information.

This nanopore based sequencing system allows direct sequencing (without amplification or cDNA preparation) if needed.


  • SARS-CoV-2 whole genome sequencing using the amplicon-based Paragon Genomics panel.
  • RNA-seq: mRNA, non coding RNA, small RNA profiling. Isoforms, splice variants and fusion transcripts analysis.
    mRNA-seq from single-cell is also available, allowing the identification of cell-to-cell differences within a population of cells. High-throughput analysis is available with the Chromium Controller system of 10x Genomics.
  • DNA-seq: genome assembly, re-sequencing (whole genome, exome or targeted -seq), structural variants identification.
  • ChIP-seq
  • ATAC-seq, MNase-seq
  • Direct detection of DNA and RNA modifications
  • 4C & HiC-seq
  • ...
Protocol used and input material
  • For classical library preparation, the Illumina TruSeq protocol is applied.
  • Poly A selection or ribo-depletion strategy can be applied to get rid of ribosomic RNA.
  • For classical protocol, a minimum of 100 ng of total RNA is required. A special protocol can be applied for lower input quantity (down to few ng).
  • A protocol of RNA exome capture is also available; ideal for low-quality samples such as FFPE samples.
  • Single-cell RNA-seq is available.
  • For whole genome sequencing, Illumina TruSeq or Nextera sample preparation protocols are applied. 50 ng of DNA input is required, or 1 ng for smaller genomes.
  • For targeted sequencing, enrichment is performed with IDT, Agilent or Twist captures.
  • For classical library preparation, the Illumina TruSeq protocol is applied.
  • Just a few ng are needed.

Before bringing samples to the Platform, please submit them in the genomics Laboratory Information Management System (LIMS) to help sample processing, monitoring and data retrieval.

Illumina NovaSeq 6000

 Illumina NovaSeq 6000
 We are grateful to the Société
 Académique de Genève
for its support.

 Photo Illumina

Oxford Nanopore Technologies MinION Mk1C

 Oxford Nanopore Technologies
 MinION Mk1C

 Photo ONT

Latest modification: 05/07/2023 - 09 h 53

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