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Bioinformatician (pipeline development), Lausanne - Switzerland

Organization
SOPHiA GENETICS
Job Location
Rue du Centre 172
1025 St-Sulpice
Switzerland
Job Description

We currently have 3 positions open in the bioinformatics and data science department of SOPHiA GENETICS in St. Sulpice/Lausanne, Switzerland. The three persons 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.

  • to create, optimise, and maintain analysis pipelines for large gene panels (e.g., whole exome)
  • to do exploratory analyses and leverage data science to assess and improve the analytical performance of our pipelines
  • one of the three positions 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
  • to assist in the setup and maintenance of CNV detection modules for a wide range of bioinformatic solutions
  • to 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
  • to perform benchmarking
Requirements
  • 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

Please note that selected candidates will need to perform a bioinformatic assignment and a self-assessment during the recruitment process. 

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