Repository for the fellowship on 3rd Generation Genomics hosted at ILRI, Nairobi.
The Biosciences eastern and central Africa – International Livestock Research Institute (BecA-ILRI) Hub (Nairobi, Kenya), together with its UK-based partners; the John Innes Centre (JIC), the Earlham Institute (EI) and Oxford Nanopore Technologies (ONT), convened this intensive training programme in genomics and bioinformatics. The aim is to equip African scientists with the skills to deploy third-generation genomics, particularly for agribiosciences. The training will largely focus on Nanopore sequencing platforms, but a general background on other sequencing platforms will be provided.
The training is designed in three phases, the first two phases being residential in ILRI (Nairobi, Kenya), and a third phase being conducted remotely at the participants’ home institutions. Below is a summary of the activities envisioned as part of this programme:
Develop phase: in the first four months, participants will be exposed to in-depth training modules on molecular biology and bioinformatics skills for 3rd generation sequencing. These training modules will comprise formal lectures and a significant fraction of hands-on sessions. Besides the series of lectures delivered by internationally recognized scientists, a team of tutors (including trainees from the 2018-2020 BixCoP) will provide ad-hoc supervision to trainees during individual and group exercises.
Demonstrate phase: intertwined with the Develop phase and extending for 1.5 month beyond it, this phase will see the trainees engage in project-based learning. They will build on the skills learnt during the Develop phase, and demonstrate their use in real-life research projects in genomics for agriculture or conservation. The projects will be co-designed with the training team.
Deploy phase: during this last phase of the training, the trainees will return to their home institution, where they will launch a small third-generation genomics unit and implement a research project to address agricultural challenges with direct relevance to their home country or region. Wherever possible, this project will be integrated into research partnerships with ILRI or another OneCGIAR institute in the home country. Trainees will benefit from the support of highly experienced mentors from the BecA-ILRI Hub, its UK-based partners, and the One CGIAR consortium. The participants are also expected to be agents of change to grow genomics and bioinformatics capacity at their institutions.
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Module 1: Unix/Linux programming - proficiency with the command line (14th - 25th of June, excluding weekends)
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Module 1: Unix/Linux programming - proficiency with the command line (14th - 25th of June, excluding weekends)
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Module 2: Python programming (28th of June - 8th of July, excluding weekends)
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Module 3: Molecular biology - DNA extraction protocols, purification, QC (12th - 14th of July)
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Module 4: 2nd and 3rd generation sequencing platforms (15th - 16th of July)
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Module 5: Nanopore library prep (19th - 20th of July)
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Module 6: Theory and practice of genome/transcriptome assembly (21st - 27th of July, excluding weekends)
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Module 7: Genome annotation (28th - 30th of July)
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Soft Skill Workshop: communication and project management (9th of July)Module 2: Python programming (28th of June - 8th of July, excluding weekends)
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Module 3: Molecular biology - DNA extraction protocols, purification, QC (12th - 14th of July)
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Module 4: 2nd and 3rd generation sequencing platforms (15th - 16th of July)
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Module 5: Nanopore library prep (19th - 20th of July)
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Module 6: Theory and practice of genome/transcriptome assembly (21st - 27th of July, excluding weekends)
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Module 7: Genome annotation (28th - 30th of July)
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Soft Skill Workshop: communication and project management (9th of July)
