Bioinformatics for Malaria Training Workshop

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Overview:
This course, which will take place at Institut Pasteur de Côte d'Ivoire, will cover bioinformatics topics related to malaria surveillance. ⁠

Intended audience:
Beginner - intermediate level bioinformaticians working with next-generation sequencing data for disease surveillance on the African continent

Purpose:
Genomic epidemiology of resistant P. falciparum training in Côte d’Ivoire with the aim to uncover the genomic signatures due to various selection pressures to be identified (host immune system? background genetics? epidemiological facies? or other). To understand the spread over the country of populations of parasites carrying any malaria drug resistant-conferring markers.

Pre-workshop training in Oct 2024. [will be conducted by Institut Pasteur de Côte d'Ivoire (I.P.C.I) team before the training] :
NGS workflows
•⁠ ⁠NGS technologies
•⁠ ⁠NGS file formats
•⁠ ⁠Linux and the command line
•⁠ ⁠shell programming
•⁠ ⁠Conda installation and use
•⁠ ⁠QC and Trimming
•⁠ ⁠Mapping, Variant calling, Explore and filter VCF

Pre-requisite:

French language is essential

Learning objective:

The course will cover:

1. Introduction to the malaria pathogen & sequencing Plasmodium genomes
2. NGS for malaria surveillance
3. Bioinformatics analysis of the Plasmodium falciparum genome
4. Malaria ⁠drug resistance surveillance in west Africa
5. Malaria biological databases
6. Population genomics and adaptive evolution in Plasmodium falciparum

Logistics:

Venue of course: Institut Pasteur de Côte d'Ivoire IPCI Health in Abidjan Côte d'Ivoire. Pullman Hotel Abidjan Plateau
Start date: 2024-11-25
End date: 2024-11-29

Bioinformatics for Malaria Training Workshop

Time	Themes	Course materials	Training partner	Interactive Sessions
09:00 - 10:00	General Malaria	Malaria, essential to guide in understanding the key concepts, behaviors malaria	Africa CDC, NGS Academy, Institut Pasteur de Côte d'Ivoire	Morning Interactive Session
11:00 - 13:00	General Malaria: Session 2	Malaria, coverage for a malaria sample compared against a reference.	Africa CDC, NGS Academy, Institut Pasteur de Côte d'Ivoire	Morning Interactive Session
14:00 - 16:00	General Malaria: Session 3	Malaria, Sample Analysis. Malaria, Sample Analysis fastqc multiqc. Malaria, fastqc nanoplot.	Africa CDC, NGS Academy, Institut Pasteur de Côte d'Ivoire	Afternoon Interactive Session

Time	Themes	Course materials	Training partner	Interactive Sessions
09:00 - 10:00	Session 1: Use cases of Malaria NGS -Drug resistance surveillance -Transmission analysis -Diagnostics resistance	Malaria, Working with fastq files	Africa CDC, NGS Academy, Institut Pasteur de Côte d'Ivoire	Morning Interactive Session
11:00 - 13:00	Session 2	Malaria, Working with fastq files results analysis	Africa CDC, NGS Academy, Institut Pasteur de Côte d'Ivoire	Morning Interactive Session
14:00 - 16:00	Session 3	Malaria, Plasmid database	Africa CDC, NGS Academy, Institut Pasteur de Côte d'Ivoire	Afternoon Interactive Session

Time	Themes	Course materials	Training partner	Interactive Sessions
09:00 - 10:00	Session 1:	Malaria, Trim file data triming	Africa CDC, NGS Academy, Institut Pasteur de Côte d'Ivoire	Morning Interactive Session
11:00 - 13:00	Targeted Sequencing, Metagenomics Session 2	Malaria, Data cleaning processes Malaria, Data analysis	Africa CDC, NGS Academy, Institut Pasteur de Côte d'Ivoire	Morning Interactive Session
14:00 - 16:00	Session 3	Malaria, Population genetic variation Malaria, Troubleshooting Malaria, Population genetics	Africa CDC, NGS Academy, Institut Pasteur de Côte d'Ivoire	Afternoon Interactive Session

Time	Themes	Course materials	Training partner	Interactive Sessions
09:00 - 10:00	Session 1:	Malaria, VC files	Africa CDC, NGS Academy, Institut Pasteur de Côte d'Ivoire	Morning Interactive Session
11:00 - 13:00	Session 2	Malaria, working in R	Africa CDC, NGS Academy, Institut Pasteur de Côte d'Ivoire	Morning Interactive Session
14:00 - 16:00	Session 3: Phylogenetic Analysis	Malaria, R	Africa CDC, NGS Academy, Institut Pasteur de Côte d'Ivoire	Afternoon Interactive Session
16:30 - 19:00	Session 3: R, Population Structure	Malaria, coding in R	Afternoon Instructor	Afternoon Interactive Session

Time	Themes	Course materials	Training partner	Interactive Sessions
09:00 - 10:00	Session 1:R, Population Genetic Analysis	Malaria, Working in R Malaria, working in R with drug resistance data malaria samples	Africa CDC, NGS Academy, Institut Pasteur de Côte d'Ivoire	Morning Interactive Session
11:00 - 13:00	Session 2 R, Population Genetic Analysis (Part 2) -Genome scans continue -Intro to genome wide association analysis	Malaria, drug resistance malaria samples in R (French)	IPCI	Morning Interactive Session
14:00 - 16:00	Session 3: Review and Feedback		IPCI	Afternoon Interactive Session
16:30 - 19:00	Session 4:Lab visit		IPCI