When:
9 am - 5 pm, 30th June - 4th July 2024
Where:
Child Health Research Foundation-Head Quarters (CHRF-HQ)
SEL Huq Skypark, 23/2 Khilji Road, Block-B, Mohammadpur,
Dhaka-1207, Bangladesh.
What:
This five-day workshop will provide participants with a comprehensive overview of bacterial genomics and its applications in antimicrobial resistance research. Through a series of lectures and hands-on sessions, participants will learn how to analyze bacterial genomes for antimicrobial resistance and virulence factors, conduct comparative genomic analysis, and apply bacterial genomics to investigate clinical and scientific problems. The workshop will focus on bioinformatic tools and software commonly used in bacterial genomic analysis. The workshop will also include setting up Linux operating system (on personal laptops), and training on basic shell commands within the Anaconda environment. The attendees are requested to bring their own laptops, so that once the training is complete, they will leave with a standard setup of bioinformatics pipelines for their own genomic investigations. The attendees are welcome to bring their own datasets as well and instructors will guide them through the analysis.
Course Outline:
Day 1: Introduction to bacterial genomics and bioinformatics
•Overview of bacterial genomics and its applications
•Introduction to bioinformatics tools for bacterial genomics analysis (e.g., NCBI/EBI databases, common file formats)
•Hands-on session: setting up Linux OS, basic Bash commands and Anaconda environment.
Day 2: Bacterial genome analysis: from sequence data to genomes
•Introduction to different sequencing methods
•Quality control of sequencing data
•De-novo genome assembly and annotation
•Submission of genomic data
•Hands-on session: Bacterial genome assembly and annotation
Day 3: Bacterial genome analysis for antimicrobial resistance
•Introduction to antimicrobial resistance and its molecular mechanisms
•Identification of resistance genes and mutations using bioinformatics tools (e.g., ResFinder, AMRfinder, CARD)
•Identification of virulence genes using different tools
•Introduction to multi-locus sequence typing (MLST) and its importance
•Hands-on session: Antimicrobial resistance and virulence gene identification, and conduct MLST-typing
Day 4: Comparative genomics and phylogenetics
•Introduction to comparative genomics and phylogenetic analysis
•Comparative analysis of bacterial genomes for identifying differences in virulence and antimicrobial resistance
•Hands-on session: Phylogenetic analysis using bacterial genomes, visualization, and annotation of phylogenetic tree
Day 5: Application of bacterial genomics
•Pathogenwatch
•Overview of current scientific and clinical applications of bacterial genomics and antimicrobial resistance testing
•Discussion of future directions and advancements in the field
•Presentations by different groups
Eligibility criterion for the course:
Must have completed or currently enrolled in Bachelors or Masters in any stream in Life Sciences, Computer Science, Bioinformatics or Public Health.
Laptop Requirements:
- Laptop with Windows needs to have 60 GB of free space (recommended 100 GB) and 8GB of RAM.
- Laptop with Mac OS needs at least 20 GB of free space.
Workshop fee:
Applicants residing in Bangladesh - BDT 15,000 (USD 140)*
Applicants residing in Low & Middle Income Countries - BDT 15,000 (USD 140)*
International applicants from High Income Countries - BDT 55,000 (USD 500)*
Participants are welcome to bring their own data for analysis! Instructors will set up participants' laptops for independent analysis.*All program fees are subject to 15% VAT as per the policy of the Government of Bangladesh.
Application deadline:
Application form will be open until _____, 2024. Interviews will be conducted the following week, and selected 12 applicants will be notified.
