gta2024-assembly.md

---

layout: event-track

title: Assembly
description: Learn all about Genome assembly. Start with the tutorial at your own pace. If you need support contact us via the Slack Channel [gta_assembly](https://gtnsmrgsbord.slack.com/archives/C07NGNT0DB5).

slack_channel: gta_assembly

contributions:
    organisers:
        - delphine-l
    instructors:
        - annasyme
        - bgruening
        - clsiguret
        - delphine-l
        - GarethPrice-Aus
        - igormakunin
        - mschatz
        - SaimMomin12
        - trungN


program:
  - section: "Introduction"
    description: |
      In this section, we will introduce what a genome assembly is, how it works, and the metrics to evaluate the quality of an assembly. **Warning: The QC training uses large data. For a lighter, faster version, follow the video and only use the sponge data**
    tutorials:
      - type: custom
        name: "[Introduction To Genome Assembly](https://youtu.be/9WZe7VGtr-k)"
        description: |
          [<i class="fas fa-video" aria-hidden="true"></i> Lecture Video](https://youtu.be/9WZe7VGtr-k) ([Slides](https://docs.google.com/presentation/d/1TPr6yKrnNj4cUb5We-E7SXAL_1h2Cqogq0tDTkgETgQ/edit?usp=sharing))
      - name: ERGA-post-assembly-QC
        topic: assembly

  - section: "Genome Assembly"
    description: |
      In this section, we will present genome assemblies for different types of organisms.
    tutorials:
      - name: mrsa-illumina
        topic: assembly
      - name: vgp_workflow_training
        topic: assembly
      - name: metagenomics-assembly
        topic: assembly

  - section: "Non-nuclear genome assembly"
    description: |
      When sequencing organisms with non-nuclear DNA, the data contain sequencing for both nuclear and non-nuclear DNA. In this section we will learn how to assemble organelles genome.
    tutorials:
      - name: mitochondrion-assembly
        topic: assembly
      - name: chloroplast-assembly
        topic: assembly

  - section: "Assembly decontamination"
    description: |
      In this section we will learn how remove sequences that do not belong to the organism you want to sequence.
    tutorials:
      - name: assembly-decontamination
        topic: assembly

---