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Genome Assembly Pipeline Overview

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About This MicroSim

This MicroSim presents the genome assembly pipeline as an animated, step-through flowchart. Students advance through each stage to understand how millions of short sequencing reads are transformed into a contiguous genome assembly.

Pipeline Stages

  1. Raw Reads — Millions of short DNA sequences (100-300 bp) from a sequencing machine
  2. QC Filter — Remove low-quality reads, trim adapters, filter contaminants
  3. K-mer Counting — Count all k-length subsequences to estimate genome size and detect errors
  4. De Bruijn Graph — Construct the assembly graph where k-mers define edges between (k-1)-mer nodes
  5. Contigs — Traverse the graph to produce contiguous sequences (contigs)
  6. Scaffolding — Use paired-end or mate-pair information to order and orient contigs
  7. Gap Filling — Fill gaps between scaffolded contigs using overlap information
  8. Final Assembly — The completed genome assembly in FASTA format

How to Use

  1. Step through — Advance through each pipeline stage to see what processing occurs
  2. Read descriptions — Each stage explains the computational methods and tools used
  3. Follow the data flow — Understand how raw reads are progressively transformed into a genome

Iframe Embed Code

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<iframe src="https://dmccreary.github.io/bioinformatics/sims/genome-assembly-pipeline/main.html"
        height="542"
        width="100%"
        scrolling="no"></iframe>

Lesson Plan

Grade Level

College introductory bioinformatics

Duration

15-20 minutes

Prerequisites

  • Understanding of DNA sequencing technologies
  • Basic concept of k-mers and sequence overlap
  • Familiarity with the de Bruijn graph concept

Activities

  1. Exploration (5 min): Step through all stages. At each, note what the input is, what processing occurs, and what the output is.
  2. Error Handling (5 min): Sequencing errors create erroneous k-mers. At which pipeline stages are errors detected or corrected? How does k-mer counting help?
  3. Discussion (5 min): Repetitive sequences (transposons, tandem repeats) are the main challenge in genome assembly. At which stage(s) do repeats cause problems? How does scaffolding help resolve ambiguities?
  4. Assessment (5 min): Answer the reflection questions below.

Assessment

  1. Why is de Bruijn graph construction preferred over overlap-layout-consensus for short-read assembly?
  2. What is the difference between a contig and a scaffold?
  3. How does k-mer counting help estimate genome size before assembly?
  4. Why are long reads (PacBio, Oxford Nanopore) sometimes used alongside short reads to improve assemblies?

References

  1. Sequence assembly — Wikipedia
  2. De Bruijn graph — Wikipedia
  3. Contig — Wikipedia
  4. Scaffolding (bioinformatics) — Wikipedia