Abstract
BackgroundThe 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.ResultsH3ABioNet 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.ConclusionThe 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.
Highlights
The Pan-African bioinformatics network, H3ABioNet, comprises 27 research institutions in 17 African countries
We identified the most important analyses as (1) variant calling on generation sequence (NGS) data; (2) 16S rRNA (16S) rDNA sequence analysis for metagenomics; (3) genome-wide association studies; and (4) imputation
The workflow requires Docker to be installed, and the Genome Analysis ToolKit (GATK) jar file and sequence reads in fastq format as input files
Summary
The Pan-African bioinformatics network, H3ABioNet, comprises 27 research institutions in 17 African countries. Processing and analysis of genomic data is an example of a big data application requiring complex interdependent data analysis workflows. Processes that were previously slow and research exclusive tasks, have become routine applications in day-to-day operations in bioinformatics and medical genomics. These advances have resulted in a biomedical data deluge with sequencing centres routinely generating data in the petabyte scale, leaving researchers and clinicians with a data processing and analysis bottleneck. Modern workflow management systems offer a high level of reproducibility, portability and computing platform independence enabling researchers to focus more on developing new methods and the interpretation of the results
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