Abstract:
BACKGROUND : The Pan-African bioinformatics network, H3ABioNet, comprises 27 research institutions in 17 African
countries. H3ABioNet is part of the Human Health and Heredity in Africa program (H3Africa), an African-led research
consortium funded by the US National Institutes of Health and the UK Wellcome Trust, aimed at using genomics to
study and improve the health of Africans. A key role of H3ABioNet is to support H3Africa projects by building
bioinformatics infrastructure such as portable and reproducible bioinformatics workflows for use on heterogeneous
African computing environments. Processing and analysis of genomic data is an example of a big data application
requiring complex interdependent data analysis workflows. Such bioinformatics workflows take the primary and
secondary input data through several computationally-intensive processing steps using different software packages,
where some of the outputs form inputs for other steps. Implementing scalable, reproducible, portable and
easy-to-use workflows is particularly challenging.
RESULTS : H3ABioNet has built four workflows to support (1) the calling of variants from high-throughput sequencing
data; (2) the analysis of microbial populations from 16S rDNA sequence data; (3) genotyping and genome-wide
association studies; and (4) single nucleotide polymorphism imputation. A week-long hackathon was organized in
August 2016 with participants from six African bioinformatics groups, and US and European collaborators. Two of the
workflows are built using the Common Workflow Language framework (CWL) and two using Nextflow. All the
workflows are containerized for improved portability and reproducibility using Docker, and are publicly available for
use by members of the H3Africa consortium and the international research community.
CONCLUSION : The H3ABioNet workflows have been implemented in view of offering ease of use for the end user and
high levels of reproducibility and portability, all while following modern state of the art bioinformatics data processing
protocols. The H3ABioNet workflows will service the H3Africa consortium projects and are currently in use. All four workflows are also publicly available for research scientists worldwide to use and adapt for their respective
needs. The H3ABioNet workflows will help develop bioinformatics capacity and assist genomics research within Africa
and serve to increase the scientific output of H3Africa and its Pan-African Bioinformatics Network.
