Module 3: Omics Analysis

This module marks the transition from computational literacy to biological discovery. After Linux fundamentals (Module 1) and environment management (Module 2), you now apply these skills to high-throughput sequencing data and complete end-to-end analysis workflows.

Learning objectives

By the end of this module, you will be able to:

• Explain the omics hierarchy and flow of information from genotype to phenotype
• Interpret the core sequencing file formats used in analysis workflows
• Run reproducible quality-control workflows with FastQC and MultiQC
• Compare de novo and reference-based assembly strategies
• Execute long-read de novo and reference-guided assembly pipelines

Lessons

• Lesson 1: The omics hierarchy and file architecture
  • Covers the biological omics layers and the FASTQ/FASTA/BAM/VCF data model
• Lesson 2: Precision quality control (QC)
  • Introduces Phred scoring, FastQC, and MultiQC interpretation
• Lesson 3: Genome assembly foundations
  • Explains assembly concepts, coverage, repeats, and tool choices
• Lesson 4: De novo assembly with long reads
  • Walks through host-read filtering, assembly with Flye, and BLAST annotation
• Lesson 5: Reference-based assembly
  • Covers mapping to ACMV references, QC metrics, and consensus generation

Note: Use your bioinfo environment for tool-heavy practical lessons.