1. HPC for large NGS data: Microbial diversity analysis
Trust Odia – Covenant University Bioinformatics Research Group - Nigeria
WACREN e-Research Hackfest – Lagos (Nigeria) 1

2. Proposed Application Architecture Data model (workflow)
Outline
introduction
motivation
Proposed Application Architecture
Data model (workflow)
Implementation strategy 2

3. NGS Sequencing : Introduction Whole genome/exome of organisms.
Large data generation (> 1000 mega base pairs, sequence length).
Various samples from DNA extraction( blood, environment etc)
Metagenomics: 16S rRNA gene
annotating unknown samples
Functional prediction of genes
Measure abundance of microbial diversity 3

4. Huse et al., 2014. BMC Bioinformatics. 15. 41

5. Bioinformatics analysis
Motivation from encountered problems
Bioinformatics analysis
High Performance Computing (program memory crash)
User analysis Flexibility (ease if use)
Sequence data issues - workaround
No Sample metadata (information) 5

6. Proposed Application architecture6

7. Data Model (Data Flow) 7

8. Linux based tools Tool Stack (technology) Several Installed Programs
python
perl
Java runtime
Available Supplementary materials
Standard of Operations (SOPs) in documentations
A bunch of scripts
Tools I am thinking of (workflow based)
BioBlend: Sloggett et al., Bioinformatics
Docker to wrap tools into an environment
Nextflow to automate workflow
Ruffus to automate workflow
Cwl and yml 8

9. High-performance computing (HPC)
Hardware: Linux 64-bit OS, > 20GB RAM and > 4 CPU cores.
> 20TB HD
Job scheduling/management
Memory allocation
Data storage 9

10. Existing system : something similar Afgan et al. , 2016
Existing system : something similar Afgan et al., Nucleic Acids Research. 10

11. The tool creation interface. The workflow creation interface.
Existing Job Management system : something similar Brown et al., PloS One.
The tool creation interface.
The workflow creation interface.
Workflow patterns.
Workflows.
Tool versioning interface. 11

12. The tool creation interface. The workflow creation interface.
Existing system : something similar Brown et al., PloS One.
The tool creation interface.
The workflow creation interface.
Workflow patterns.
Workflows.
Tool versioning interface. 12

13. Thank you!
sci-gaia.eu 13