Bioinformatics Engineer

Watchmaker Genomics

Watchmaker Genomics

Other Engineering
Cape Town, South Africa
Posted on Tuesday, June 11, 2024

Position: Bioinformatics Engineer

Position Type: Full-Time Employee

Location: Cape Town, South Africa (onsite at Salt River location)

Experience: Undergrad with 4+ Years experience, Hons with 2+ years experience, or M.Sc or PhD with a year of relevant experience.

Watchmaker Genomics is inviting applications for the full-time position of Bioinformatics Engineer, based in Cape Town, South Africa.

This position reports to the Cape Town Senior Bioinformatics Scientist, and will be responsible for robust internal analytics and software development. This individual will support projects involving the design, development, and implementation of novel algorithms for analyzing large sequencing data sets, enabling the extraction of information on the functionality of novel enzymes for RNA/DNA manipulation, and modules or kits for analysis of nucleic acids in a variety of experimental contexts. This role will contribute to the development of automated analytical pipelines and requires rigorous, solution development and testing experience. The ideal candidate will have a firm understanding of the basic molecular biology of sequencing library preparation and scalable software development practices.

The successful candidate will thrive in a dynamic, fast-paced working environment and contribute directly to our company culture and success. The position provides an opportunity to gain valuable experience in both innovative bioinformatics and computational biology as they relate to the development of high quality products for genomics, in addition to the development of robust internal infrastructure to enhance our R&D efficiency.


  • Contribute to a highly innovative and efficient R&D computational biology program
  • Develop novel algorithms for the analysis of a wide variety of data sets
  • Be a key contributor to a well-engineered and documented code base
  • Produce code that is robust, automatable, and repeatable
  • Contribute to strategies for efficient data analysis for the purpose of maximizing learning from new and historical datasets
  • Identify opportunities for internal process improvement

Skills and Requirements

The candidate should have an undergraduate degree in bioinformatics, computational biology, mathematics/statistics, computer science, engineering, physics or similar relevant field. Relevant industry experience or relevant higher degrees (hons, M.Sc, Phd) are preferred.

The candidate must have a foundation in quantitative data analysis and problem solving. Advanced software engineering skills are required. A basic understanding of biological sample sequencing and areas including structural biology and data extraction from large biological databases is a plus.

The following skills and experience are requirements:

  • Expertise in Python is required
  • An understanding of source control using git is required
  • A basic foundation in statistics is required
  • Strong interpersonal skills and an ability to work as an effective member of a goal-oriented team
  • Adept and creative problem-solving skills
  • Ability to plan, build, troubleshoot and complete solutions to data problems
  • Excellent organizational skills and outstanding attention to detail
  • Excellent written and verbal communication skills
  • Adept at data wrangling
  • Familiarity with software testing frameworks

The following skills and experience are beneficial for the position:

  • Familiarity with at least one statically typed languages such as C++, Java, or Rust
  • An understanding of existing tools for sequencing data analysis
  • Understanding of bioinformatics algorithms and best practices
  • Ability to develop solutions using machine learning techniques
  • A basic understanding of molecular biology techniques such as PCR and sequencing library preparation
  • Demonstrated ability to plan, build, troubleshoot and complete self-created software solutions to advanced data analysis problems, preferably including ML techniques.

Our stack

We utilize AWS for storage, compute and other services, Jenkins for CI/CD, Postgres as our flavor of db, Nextflow for pipelines, and Python as our main development language. We use a combination of horizontal and vertical scaling as the need dictates. Version control is with git, and repos on GitHub.


  • An undergraduate degree in bioinformatics, computational biology, mathematics, statistics, computer science, engineering, physics or related relevant fields is required.
  • Relevant industry experience or relevant higher degrees (hons, M.Sc, Phd) are preferred.

Application Procedure

To apply for the position, please submit the following in a PDF format Indeed Link and Pnet Link

  • Letter of motivation
  • Resume or Curriculum vitae, highlighting relevant qualifications and experience

Applications without a Letter of Motivation will not be considered. Local candidates preferred.

If selected to participate in the interview process, the names and contact information of three professional references who are able to assess your suitability for the position in terms of the specified requirements will be requested.


Watchmaker Genomics is committed to being an equal opportunity employer and creating a culturally diverse environment. All qualified applicants will receive consideration for employment without regard to race, color, religion, gender, gender identity or expression, sexual orientation, national origin, genetics, disability status, age, or veteran status or any other characteristics as protected by applicable law.

All applicants will be asked if currently eligible to work in South Africa; and if now or in the future will require visa sponsorship to continue working in South Africa.

This position may be subject to pre-employment checks, including driving history check, drug screening and a background check for any convictions directly related to its duties and responsibilities. All pre-employment checks will comply with all applicable laws.