High-throughput DNA sequencing-concepts and limitations, Bioessays, vol.32, issue.6, pp.524-560, 2010. ,
Ten Simple Rules for Reproducible Computational Research, PLoS Comput Biol, vol.9, issue.10, 2013. ,
Use of application containers and workflows for genomic data analysis, J Pathol Inform, vol.7, issue.1, p.53, 2016. ,
A review of bioinformatic pipeline frameworks, Brief Bioinform, vol.18, issue.3, pp.530-536, 2017. ,
Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses, J Biomed Inform, vol.49, pp.119-152, 2014. ,
Enabling the genomic revolution in Africa, Science, vol.344, issue.6190, pp.1346-1354, 2014. ,
, Genome Res, vol.26, issue.2, pp.271-278, 2016.
Common Workflow Language, v1.0. doi.org, 2016. ,
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences, Genome Biol, issue.8, p.11, 2010. ,
Rabix: an Open-Source Workflow Executor Supporting Recomputability and Interoperability of Workflow Descriptions, Pac Symp Biocomput, vol.22, pp.154-65, 2016. ,
A scalable data analysis platform for metagenomics, IEEE international conference on Big Data. IEEE, pp.21-27, 2013. ,
Nextflow enables reproducible computational workflows, Nature Biotechnology, vol.35, pp.316-325, 2017. ,
Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders, N Engl J Med, vol.369, issue.16, pp.1502-1513, 2013. ,
Whole-genome and whole-exome sequencing in neurological diseases, Nat Rev Neurol, vol.8, issue.9, pp.508-525, 2012. ,
Application of Whole Exome Sequencing in the Clinical Diagnosis and Management of Inherited Cardiovascular Diseases in Adults, Circ Cardiovasc Genet, vol.10, issue.1, 2017. ,
The genome analysis toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res, vol.20, issue.9, pp.1297-303, 2010. ,
A framework for variation discovery and genotyping using next-generation DNA sequencing data, Nat Genet, vol.43, issue.5, pp.491-501, 2011. ,
From fastQ data to high-confidence variant calls: The genome analysis toolkit best practices pipeline, Current Protocols in Bioinformatics, 2013. ,
Trimmomatic: A flexible trimmer for Illumina sequence data, Bioinformatics, vol.30, issue.15, pp.2114-2134, 2014. ,
Aligning sequence reads, clone sequences and assembly contigs with BWAMEM, 2013. ,
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3, Fly, vol.6, issue.2, pp.80-92, 2012. ,
ClinVar: Public archive of relationships among sequence variation and human phenotype, Nucleic Acids Res, 2014. ,
Analysis, Optimization and Verification of Illumina-Generated 16S rRNA Gene Amplicon Surveys, PLoS ONE, vol.9, issue.4, p.94249, 2014. ,
Phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data, PLoS ONE, vol.8, issue.4, 2013. ,
Quality Control Procedures for Genome-Wide Association Studies, Current Protocols in Human Genetics, 2011. ,
The AWK Programming Language, 1987. ,
A General Approach for Haplotype Phasing across the Full Spectrum of Relatedness, PLoS Genet, vol.10, issue.4, 2014. ,
A flexible and accurate genotype imputation method for the next generation of genome-wide association studies, PLoS Genet, vol.5, issue.6, 2009. ,
H3Africa AWI-Gen Collaborative Centre: a resource to study the interplay between genomic and environmental risk factors for cardiometabolic diseases in four sub-Saharan African countries, Glob Health Epidemiol Genomics, vol.1, issue.20, 2016. ,
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update, Nucleic Acids Res, vol.44, issue.W1, pp.3-10, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01360125
The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud, Nucleic Acids Res, vol.41, 2013. ,
Integrating Taverna and Galaxy workflows with cloud computing support, BMC Bioinforma, vol.13, issue.1, 2012. ,
Automated quality control for genome wide association studies, F1000Research, vol.5, p.1889, 2016. ,
A cloud-based GWAS analysis pipeline for clinical researchers, pp.387-94, 2014. ,
Genome-wide association studies pipeline (GWASpi): A desktop application for genome-wide SNP analysis and management, Bioinformatics, vol.27, issue.13, pp.1871-1873, 2011. ,