Course Description: Mapping and Variant Calling of Short MTBC Reads

The Mapping and Variant Calling of Short MTBC Reads course provides participants with the essential skills to process and analyze Mycobacterium tuberculosis complex (MTBC) short-read sequencing data. Using Illumina sequencing data, participants will learn how to map reads to a reference genome and identify genetic variants that contribute to drug resistance and strain diversity.

This course is designed for researchers and students in bioinformatics and genomic epidemiology, equipping them with computational skills to perform accurate mapping and variant calling using widely used bioinformatics tools.

What You’ll Learn

• Read Mapping Techniques: Aligning short reads to the MTBC reference genome using BWA-MEM and Bowtie2.
• Variant Calling: Identifying single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs) using tools like GATK, FreeBayes, and Samtools.
• Quality Control: Assessing read quality and alignment accuracy with FastQC and Qualimap.
• Interpreting Variant Calls: Understanding the impact of genetic variations on drug resistance and strain evolution.
• Hands-On Training: Running pipelines for mapping, variant calling, and annotation using Illumina sequencing data.

By the end of this course, participants will be able to process and analyze MTBC sequencing data, facilitating research in genomic epidemiology and drug resistance surveillance.