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

Version: 1, Uploaded by: Administrator, Date Uploaded: 25 November 2022

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Reference (Identifier)

GS-00518

Title

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

Broad Theme Classification

2. Engineering and Technology

Second Level Classification

2.6 Medical Engineering

Country Specific Sectors

28. Other

Author Name

Dr. Shakuntala Baichoo

Institution

University of Mauritius

Co-Author 1 Name

Yassine Souilmi

Co-Author 2 Name

Sumir Panji

Co-Author 3 Name

Gerrit Botha

Co-Author 4 Name

Ayton Meintjes

Co-Author 5 Name

Scott Hazelhurst

Co-Author 6 Name

Hocine Bendou

Co-Author 7 Name

Eugene De Beste

Co-Author 8 Name

Phelelani T. Mpangase

Co-Author 9 Name

Oussema Souiai

Co-Author 10 Name

Mustafa Alghali

Co-Author 11 Name

Long Yi

Co-Author 12 Name

Brian D O’Connor

Co-Author 13 Name

Michael Crusoe

Co-Author 14 Name

Don Armstrong

Co-Author 15 Name

Shaun Aron

Co-Author 16 Name

Fourie Joubert

Co-Author 17 Name

Azza E Ahmed

Co-Author 18 Name

Mamana Mbiyavanga

Co-Author 19 Name

Peter Van Heusden

Co-Author 20 Name

Lerato E. Magosi

Co-Author 21 Name

Jennie Zermeno

Co-Author 22 Name

Liudmila Sergeevna Mainzer

Co-Author 23 Name

Faisal M. Fadlelmola

Co-Author 24 Name

C. Victor Jongeneel

Co-Author 25 Name

Nicola Mulder

Page Range

1-13

Date Published

29 November 2018

Abstract

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.

Keywords

Workflows,Pipeline,Bioinformatics,Africa,Genomics,Docker,Reproducibility

Language

English

Publisher

Springer

Content Classification

Journal Article

Note/Remarks

Source: Google Scholar

Date Uploaded

25 November 2022

Size

File Format

Hyperlink

Journal

BMC Bioinformatics

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