Building portable pipelines for reproducible scientific workflows: The H3ABionet Pipelines Project on E n

<div>Presentation given by Scott Hazelhurst at Galaxy Africa 2018 (Cape Town, South Africa)</div><div><br></div

Characterization of POR haplotype distribution in African populations and comparison with other global populations: Supplementary tables

Background & aim: POR is an enzyme that mediates electron transfer to enable the drug-metabolizing activity of CYP450 proteins. However, POR has been understudied in pharmacogenomics despite this vital role. The authors aimed to characterize the genetic variation in POR across African populations and to compare the star allele (haplotype) distribution with that in other global populations. Materials & methods: POR star alleles were called from whole-genome sequencing data using the StellarPGx pipeline. Results: In addition to the common POR*1 and *28 haplotypes (defined by rs1057868), five novel rare haplotypes were computationally inferred. No significant frequency differences were observed among the majority of African populations. However, POR*28 was observed at a higher frequency in individuals of non-African ancestry. Conclusion: This study highlights the distribution of POR alleles in Africa and across global populations with a view toward informing future precision medicine implementation.</p

Additional file 4: Fig. S1. of Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data

Pearson correlations (with p-values) and Mann-Whitney-Wilcoxon non- parametrical test p vales between array data with 1 heterozygous SNP per ROH and WGS with 1 to 5 heterozygous SNPs per ROH. (JPEG 1011 kb

Additional file 1: Table S1. of Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data

Mean number of SNP (in homozygous state) per ROH in array data with 1 heterozygous SNP per ROH and WGS data with 1 to 5 heterozygous SNPs per ROH. ep(P,h) values for different populations P and allowed heterozygous SNP. (DOCX 22 kb

Computational requirements for running the H3ABioNet GWAS workflows. - Lecture 1 H3ABioNet 2018 GWAS Lecture series

Computational requirements for running the H3ABioNet GWAS workflows The first of a series of seven online lectures for Genome Wide Association Studies (GWAS) will cover the technical requirements for setting up a your computational environment for running the H3ABioNet GWAS workflows. In this inaugural lecture of the series, Prof. Hazelhurst will cover the the following topics: 1. Installing and using Nextflow 2. Installing and using Github 3. Use of containers for packaging and running tools 4. Pulling the GWAS pipeline from Github and running it As this lecture aims to provide attendees with an environment to the run the H3ABioNet GWAS workflow at their own pace, there are some preliminary software requirements: 1. Either a Linux machine or an Apple running macOS 2. Ideally you should have machine with at least 2-4 cores and 8GB of RAM. 3. Java 8 4. Nextflow installed (see installation instructions at https://www.nextflow.io/) 5. Python 3 Please also install either Docker OR the following dependencies using pip3: Pandas, Matplotlib, Openpyxl, SciPy, NumPy PLINK 1.9 [Please also refer to the following documentation to obtain the H3ABioNet GWAS workflow]: https://github.com/h3abionet/h3agwas/blob/master/README.md </div

H3ABioNet_reproducible_workflows_project_SciDataCon_Nov_2018.pdf

Presentation of the H3ABioNet Bioinformatics Workflows for reproducible science provided at the SciDataCon International Data Week in Gaborone, Botswana November 2018. <br

The policy, infrastructure, training, and funding landscape of computational biology in South Africa (2000–present).

<p>Government policy on computational biology was driven largely by the DST (above timeline arrow), while bioinformatics training courses have been a constant feature of this landscape since 2003. There was a major period of infrastructure investment from 2002–2007, from the NBN, but national funding has now become available only every two years. National bioinformatics conferences also occur in two-year intervals (details in text).</p

Bioinformatics degree programs offered at some of the South African universities.

<p>The numbers shown are for registrations or graduations where the content is bioinformatics. The key research areas of each institution are included.</p