Research Officer I – Bioinformatics at International Livestock Research Institute (ILRI)

Key Responsibilities

• Perform computational analyses of complex genomics and other ‘-omics’ datasets (sequence alignments, FASTA, SAM/BAM and VCF files, phylogenetic trees, etc), provide synthetic and graphical representations of the results, and interpret the same
• Drive post-sequencing analyses (whole-genome reconstruction at chromosome or telomere-to-telomere level) based on long reads obtained from ILRI’s Oxford Nanopore Technologies platform.
• Help scientists design and run their experiments on the same platform
• Make the most effective use of the computational resources on ILRI’s High Performance Cluster; participate actively in the development of in-house scripts and pipelines to be hosted on BecA’s GitHub account and other ad-hoc storage space. Use and develop Nextflow/Airflow pipelines whenever necessary
• Participate in the designing, planning and delivering capacity building activities such as short training workshops, seminars, bioinformatics Communities of Practice, etc
• Provide informed advice to the Head of Data & Research Methods on questions pertaining to the maintenance and development of the bioinformatics platform (on both hardware and software aspects)
• Contribute to the resource mobilisation efforts, be they in human resource (e.g. recruiting external trainers for workshops) or financial resource (e.g. writing grant proposals)
• Support student supervision and academic capacity-building activities, especially in the frameworks of the One CGIAR Initiatives
• Perform any other related duties as may be required

Requirements

• Masters degree in computer science, data science, bioinformatics, computational biology, biotechnology, biostatistics or a relevant field.
• Three years relevant experience with at least some analysis work performed based on 454, Ion Proton, Illumina, Oxford Nanopore or PacBio sequencing data.
• Excellent working knowledge of GNU/Linux systems such as Debian/Ubuntu or CentOS
• Ability to read and write programs fluently in at least two of the following languages: Python, Bash, R, Perl
• Experience with distributed computing environments with load schedulers such as SLURM, SGE or Torque
• Experience with modern version-control platforms for collaborative coding such as GitHub
• A good understanding of the principles of molecular biology
• A good understanding of the principles of molecular evolution and the ability to perform phylogenetics/phylogeographics reconstruction
• An excellent attention to detail that needs to be put constantly in use, especially regarding programming
• Familiarity with bioiformatics tools for genome assembly and variant calling
• Familiarity with the Oxford Nanopore technology platform will be an added advantage
• Familiarity with at least one workflow management system like Nextflow, SnakeMake or Airflow
• Knowledge of at least one GUI-based boinformatics suite such as CLC Genomics Workbench, UGENE, Mega, etc.