Welcome to HackBio

• Welcome to HackBio
• The New Platform: Learning
• Testing the Platform
• Getting Help

Recap on NGS method

• Welcome to the Exciting World of Next-Generation Sequencing in Genomics!
• Setting up your PC.
• Why Bash!
• Downloading files with wget
• Managing Folders (Directories)
• Creating and Reading Files with touch
• Copy, Paste and Delete
• Changing Directories
• Finding Patterns with grep
• Final Tips and Tricks
• BASH
• Introduction to BASh
• Links and Resources
• Setup for anaconda for specific tasks/pipelines on Linux (Optional)

NGS Data Pipeline: Quality Control

• What is Data Preprocessing
• First thing to do with your sequencing data
• Performing Quality Control with FastQC
• Understanding FastQC Reports
• Aggregating your FastQC Reports for Multiple Datasets
• MultiQC Usage
• Using WGET to download our fastQ dataset from GitHub
• Quality Control
• Link to resources

NGS Data Pipeline: Trimming

• Introduction to Data Trimming
• Trimming off Low Quality Reads
• Implementing FastP
• Trimming

NGS Data Pipeline: Genome Mapping

• Introduction to the Genome Mapping
• Introduction to Genome Mapping
• Building Genome Maps: BWA Usage
• Automating BWA Implementation
• Genome Mapping
• Link to resources

Manipulating Your Alignment Map

• Manipulating Your Alignment Map
• The Nature of SAM/BAM files
• Sorting BAM Files
• SAM vs BAM files: Interconversion and Manipulation
• Alignment Maps

Handling Bacterial (Haploid) Genomes

• Variant Calling
• Implementation for Haploid Genomes
• Preparing Starting Files and Coding Environment
• Variant Calling
• Viewing the result (See next slides to see expected outputs)
• Expected Results

Project Section

• Searching for Mutations Leading to Isoniazid Resistance in TB