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Bioinformatics Scientist

Date: Feb 23, 2021

Location: Philadelphia, PA, US

Company: Spark Therapeutics

Join the Spark Team


We were born of innovation, springing from the curiosity, imagination and dedication of remarkable scientists and healthcare visionaries. Our shared mission is to challenge the inevitability of genetic disease by discovering, developing, and delivering treatments in ways unimaginable – until now.


We don’t follow footsteps. We create the path.


The Data Science Group at Spark Therapeutics is seeking an NGS Bioinformatics Scientist to join its bioinformatics team. He/She will play a key role in expanding next-generation sequencing bioinformatics capabilities with the following responsibilities:

  • Collaborate with research scientists in all phases of NGS including experimental design, bioinformatics, and data analysis
  • Design, implement, and operate bioinformatics pipelines for read alignment/mapping, QC, variant calling, structural variant calling RNA-seq expression and other NGS applications from short read and long read data
  • Identify, evaluate, and integrate open source and commercial bioinformatics NGS software packages to continuously improve NGS pipelines
  • Engage in cross-functional discussions, providing conceptual input in experimental and study design and serve as subject matter expert in NGS bioinformatics
  • Collaborate with the Software & Data Engineering team to translate early-stage bioinformatics pipelines into production grade, scalable, and cloud ready pipelines
  • Summarize, visualize, and communicate bioinformatics analyses to key stakeholders



  • M.S. or Ph.D. in Computational Biology, Bioinformatics, Computer science or related disciplines
  • 3-5 years of experience in bioinformatics (Ph.D. research years can count as experience)
  • Minimum 2 years of experience in building bioinformatics pipelines for next generation sequencing (NGS) for short-read (Illumina) and long read (Oxford Nanopore and Pacbio) platforms



  • Deep understanding of next generation sequencing methods, platform-specific bias and errors, and data interpretation
  • Hands-on experience with genome alignment, mapping, variant calling, and QC/annotation tools
  • Excellent understanding of molecular and cell biology
  • Proficiency in programming using one or more common bioinformatics languages such as Python
  • Experience with using commonly used genomic databases UCSC Genome Browser, NCBI/RefSeq, Enembl
  • Expertise with commonly used bioinformatics tools such as BWA, minimap2, Samtools, BLAST, GATK suite
  • Experience using bioinformatics workflow technologies such as WDL, CWL, Cromwell, Docker is preferred
  • Strong familiarity with core concepts in molecular biology and related lab technologies
  • Track record of following best practices of coding, version control, and code documentation
  • Experience with AAV vectors and gene therapy is preferred, but not required
  • Self-motivated to learn and develop new methodologies, manage multiple analysis pipelines simultaneously, keep accurate records, follow instructions, and comply with company policies
  • Excellent communication skills (both oral and written)
  • Works with colleagues as a team player
  • Experience managing external collaborations is a plus

Nearest Major Market: Philadelphia