Module 7: Data Analysis and Experimental Design

MB 360: Scientific Inquiry in Microbiology At the Bench

Carlos C. Goller, Ph.D.

NC State University | Department of Biological Sciences

Camila Loyola, Graduate Teaching Assistant

2026-08-19

Module 7: Data Analysis and Experimental Design

MB 360: Scientific Inquiry in Microbiology At the Bench

MB 360 Lab Workbook
NC State University | Department of Biological Sciences

Overview

Weeks 13–14 · Genome assembly · Annotation review · Comparative analysis · Phenotype connection

  • Submit an assembly job to BV-BRC
  • Apply bioinformatics tools to assemble and annotate genomes
  • Connect genomic results back to phenotypic evidence

Learning Outcomes

  • Explain the purpose of bioinformatics tools and workflows used
  • Discuss the significance of genome assembly
  • Practice using web-based bioinformatics tools
  • Explore genome assemblies and annotations
  • Collect and interpret genomic data in the context of phenotypic analyses
  • Revise the draft for the individual and group projects

Skills & Knowledge

Skills

  • Perform sequence-read quality review
  • Assemble microbial genomes
  • Annotate and explore genome content

Knowledge

  • Steps required to assemble a microbial genome
  • Tools for filtering, assembly, annotation, and metabolic modelling
  • Cloud-based bioinformatics workflow submission

Background

Workflow diagram showing how sequencing data moves into assembly, annotation, and comparative analysis.

Sequencing-analysis pipeline for genome assembly and comparative interpretation.

Compare your isolate to Delftia acidovorans SPH-1 and related public genomes to identify genetic features that explain observed growth and metabolic behaviour.

Lab Safety

This is a bioinformatics lab — no live organisms or chemicals are used today.

Methods: Genome Assembly (BV-BRC)

  1. Access the shared BV-BRC workspace
  2. Obtain the concatenated read files for your isolate
  3. Run the Comprehensive Genome Analysis workflow
    (long-read + paired short-read data)
  4. Create an output folder labelled with the isolate name
  5. Submit the job and monitor the results
  6. Upload the assembled FASTA file to SeqHub

Methods: Genome Comparisons

  • Use Similar Genome Finder in BV-BRC
  • Compare your isolate against representative and public genomes
  • Save result tables and pie-chart images