Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics

 

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dc.contributor.author Baichoo, Shakuntala
dc.contributor.author Souilmi, Yassine
dc.contributor.author Panji, Sumir
dc.contributor.author Botha, Gerrit
dc.contributor.author Meintjes, Ayton
dc.contributor.author Hazelhurst, Scott
dc.contributor.author Bendou, Hocine
dc.contributor.author Beste, Eugene d
dc.contributor.author Mpangase, Phelelani T
dc.contributor.author Souiai, Oussema
dc.contributor.author Alghali, Mustafa
dc.contributor.author Yi, Long
dc.contributor.author O’Connor, Brian D
dc.contributor.author Crusoe, Michael
dc.contributor.author Armstrong, Don
dc.contributor.author Aron, Shaun
dc.contributor.author Joubert, Fourie
dc.contributor.author Ahmed, Azza E
dc.contributor.author Mbiyavanga, Mamana
dc.contributor.author Heusden, Peter v
dc.contributor.author Magosi, Lerato E
dc.contributor.author Zermeno, Jennie
dc.contributor.author Mainzer, Liudmila S
dc.contributor.author Fadlelmola, Faisal M
dc.contributor.author Jongeneel, C. V
dc.contributor.author Mulder, Nicola
dc.date.accessioned 2018-12-11T14:07:58Z
dc.date.available 2018-12-11T14:07:58Z
dc.date.issued 2018-11-29
dc.identifier.citation BMC Bioinformatics. 2018 Nov 29;19(1):457
dc.identifier.uri https://doi.org/10.1186/s12859-018-2446-1
dc.identifier.uri http://hdl.handle.net/11427/29136
dc.description.abstract 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.
dc.language.iso en
dc.publisher BioMed Central
dc.subject.other Workflows
dc.subject.other Pipeline
dc.subject.other Bioinformatics
dc.subject.other Africa
dc.subject.other Genomics
dc.subject.other Docker
dc.subject.other Reproducibility
dc.title Developing reproducible bioinformatics analysis workflows for heterogeneous computing environments to support African genomics
dc.type Journal Article
dc.date.updated 2018-12-02T04:11:18Z
dc.rights.holder The Author(s)


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