Bioinformatician (pipeline development), Lausanne - Switzerland

In our journey to impact on patients' lives, we currently have an open position in the bioinformatics and data science department of SOPHiA GENETICS in St. Sulpice/Lausanne, Switzerland. This person we are looking for will work on "pipeline development", i.e. on designing workflows to accurately and efficiently process large NGS datasets produced in the clinical context in order to diagnose genomic alterations.


As a Bioinformatician for the pipeline development team you create, optimise, and maintain analysis pipelines for large gene panels (e.g., whole exome). You do exploratory analyses and leverage data science to assess and improve the analytical performance of our pipelines.

You will focus in particular on the integration of specialised, cutting-edge analyses such as somatic variant analysis, tumor/normal comparisons, CNV detection, TMB analysis, and MSI detection. 

Additionally, you implement solutions that meet the particular challenges associated with the analysis of very large data sets (e.g. entire Novaseq runs), in particular in terms of run time and resource usage, you assist in the setup and maintenance of CNV detection modules for a wide range of bioinformatic solutions and you perform benchmarking.

Your profile

  • PhD and/or several years postdoc or industry experience in bioinformatics and NGS data analysis
  • fluency in R and ideally in another language such as Python, C++, or Perl
  • proven track record of working with high performance computing clusters, bioinformatic analysis pipelines, version control systems, and parallel computing
  • solid knowledge of best practices for software development and testing
  • ability to approach complex problems in a systematic fashion and from a software engineering and technical implementation point of view
  • capacity to work in a fast-paced multidisciplinary and multicultural environment

We offer

  • Young and closely interacting R&D team in a casual working environment
  • Career opportunities in a fast-growing company with worldwide reputation
  • International and multicultural environment
  • A stimulating technical environment (cloud computing, Big Data, CI, CD, ...);
  • Permanent exchanges with teams of experts within the company (AI, genomics, medicine, etc.);
  • Flexible hours, home office opportunities, etc. ;

Starting date: ASAP (or to be decided)

Contract type : CDI full-time

Application process

If you think you fit this position, please send a CV and a cover letter. Please note that incomplete applications will not be considered.

After an initial screening process, candidates will be invited for remote interviews. Selected candidates will then be invited for personal interviews.