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Biotechnology Program (BIT)

BIT 495/595 Portable Genome Sequencing

Nature Methods named long-read sequencing “The Method of 2022” for its impact on countless projects and applications, including the Telomere-to-Telomere (T2T) human genomes and rapid diagnostics. We will create and share work on this webpage as part of the course.

Nanopore devices sequencing
Oxford Nanopore Technologies (ONT) sequencing devices are becoming more accessible and generating large amounts of sequencing data. What and where can these and other devices be used for? Photo by Carlos C. Goller.

Overview

  1. Evaluate sample preservation and nucleic acid extraction procedures for a given experiment.
  2. Analyze Nanopore sequence data to base call signals and filter reads.
  3. Compare sample and library preparation methods for a given sample and research question.
  4. Design an experiment to address a relevant biological question with Nanopore sequencing.

Topics

  • Topic 1: Nanopore sequencing technology and applications.
  • Topic 2: Sample storage and prep. DNA and RNA extraction options and quality control
  • Topic 3: Library Prep for DNA and RNA
  • Topic 4: Base-calling 
  • [Data analysis time]
  • Topic 5: Workflows & analyses
  • Topic 6: New Applications 

Labs

  • Lab 1: Sample prep and quality control
  • Lab 2: Plasmid sequencing and confirmation
  • Lab 3: Microbial genome sequencing and assembly
  • Lab 4: Metagenome sequencing
  • [Open lab time]
  • Lab 5: RNA sequencing
  • Lab 6: Large genome sequencing 

Resources

Oxford Nanopore Technologies (ONT) M1kC
Oxford Nanopore Technologies (ONT) sequencer