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Bioinformatics Pipeline Engineer (Linux) (Contract)

: Mahidol Oxford Tropical Medicine Research Unit (MORU)

: Nonprofits / องค์กรไม่แสวงหาผลกำไร

: 838

: 13 February 2025

28 February 2025

Vacant position: Bioinformatics Pipeline Engineer (Linux) (Contract)

Mahidol Oxford Tropical Medicine Research Unit (MORU)

Faculty of Tropical Medicine, Mahidol University

Job title           Bioinformatics Pipeline Engineer

Location          MORU – Bangkok

Terms              Consultancy Contract

Duration          Until 31 January 2026, the contract may be extended subject to funding availability and performance

 

About the GenRe-Mekong project

MORU is a collaboration between Mahidol University (Thailand), Oxford University (UK) and the UK's Wellcome Trust. For over 40 years, MORU has conducted targeted clinical trials and public health research that aim to discover and develop appropriate, affordable interventions that measurably improve the health of people living in resource-limited parts of the world.

The MORU Malaria Genomics group leads GenRe-Mekong (“Genetic Reconnaissance of Malaria in the Malaria in the Greater Mekong Subregion”), a large-scale malaria genetic surveillance project, providing National Malaria Control Programmes (NMCPs) in the Greater Mekong Subregion with timely and actionable knowledge to support their decision-making in malaria elimination efforts. GenRe-Mekong collaborates with NMCPs in four countries to collect dried blood spot samples from malaria patients. Using these DBS samples, malaria genomes are processed by an Amplicon genotyping platform using Illumina sequencing, to generate high-resolution genetic data. We analyse information on the genetics of the parasites, such as monitoring drug-resistance mutations and tracking resistant strains. This information is reported back to public health decision-makers to inform and enhance malaria control and elimination strategies.

More about us: https://genremekong.org/

 

Job Description

GenRe-Mekong processes genomic data from Plasmodium falciparum (Pf) and Plasmodium vivax (Pv) to advance malaria research and support malaria control and elimination. So far, the project has relied on bioinformatic pipelines for sample processing that are managed by research partners. To enhance sustainability and flexibility, and to support other surveillance projects, we now aim to implement our own cloud-based processing pipelines, building on existing frameworks such as  https://github.com/vivaxgen/MicroHaps and https://github.com/malariagen/pipelines.

We are seeking a skilled Bioinformatic Pipeline Engineer to adapt, deploy and optimise this cloud-based solution, ensuring scalable, manageable and accessible genomic data processing for our team and collaborators. They will ensure that the outputs from the pipelines are of the high quality required to support public health decision-making, and will support the management, archiving and security of data and metadata pertaining to the samples.

 

Principal Responsibilities

  1. Pipeline development and maintenance:
  • Design, implement, and optimise automated bioinformatics pipelines for malaria genetic data processing.
  • Ensure pipeline efficiency, accuracy, scalability and security for large-scale genomic datasets.
  1. Data processing and quality control
  • Process raw genetic sequencing data and perform quality control to ensure correctness of results, and enable accurate downstream analyses.
  • Work closely with the data analysis team to gather and implement new requirements, and address any quality issues.
  • Put in place an issue management system that will track pipeline issues to completion.
  1. Training and support
  • Train and support team members in pipeline usage and troubleshooting.
  • Collaborate with the PI and team to align pipelines with project objectives.
  1. Documentation
  • Maintain detailed documentation of workflows, configurations, and processes for reproducibility.
  • Generate reports on pipeline performance, results, and troubleshooting activities.

 

Required Skills

  • Solid experience and proficiency in using Linux command-line environments.
  • Linux system management skills, including installing and configuring systems and software.
  • Familiarity with R and Python, or willingness to learn and work with these tools.
  • Strong English-language comprehension and communication skills.
  • Able to work both independently and collaboratively as part of a team.

 

Preferred (Optional) Skills

  • Familiarity with sequence analysis techniques.
  • Basic knowledge of statistics.

 

How to apply

    • Please submit a cover letter and CV to pannapat@tropmedres.ac
    • On your email subject, please state: Application for Bioinformatics Pipeline Engineer (Linux) and full name
    • The closing date:  28 February 2025

 

Terms of employment

This position is offered on a consultancy contract basis with an initial offer until the end of project fund availability in January 2026. The continuing yearly fixed-term contract will be offered based on performance and subject to funding availability. 

** Note for international applicants: This position requires residency in Bangkok. Visa and work permits are not provided, and employment will be offered on a consultancy basis with a local salary. **

 

The successful applicant should have good communication skills. Interested applicants, please submit your application with detailed resumé email and subject, please state:

Application for Bioinformatics Pipeline Engineer (Linux) and full name to

Khun Pannapat Masingboon (Email: pannapat@tropmedres.ac)

Mahidol-Oxford Tropical Medicine Research Unit (MORU)

Faculty of Tropical Medicine, Mahidol University

420/6 Rajvithi Road, Bangkok 10400

 

MORU’s Commitment to Equity, Diversity, and Inclusion

MORU is committed to creating an inclusive culture and a respectful environment, and values diversity and promoting equity for all its members. MORU does not tolerate any form of harassment or victimisation

and expects all members, visitors and contractors to treat each other with respect, courtesy and consideration. Successful candidates are expected to adhere to these standards and principles.

Contact : Khun Pannapat Masingboon (Email: pannapat@tropmedres.ac)


ที่ปรึกษา / Consultant