GenEpi-BioTrain - Virtual training 05: Bacterial genome assembly and quality control

Topic outline

• Bacterial genome assembly and quality control (GenEpi-BioTrain - Virtual training 5)

  Bacterial genome assembly and quality control (GenEpi-BioTrain - Virtual training 5)

  ℹ️ Please Note

  You are welcome to explore the available resources and video recordings. Please note that the resources in this course come from the Virtual Training 05 held in December 2023, and certificates are only issued to participants who attended the live webinar sessions.

  Welcome to this virtual training space on EVA.

  Below you will see the two online sessions and their support materials.

  In anticipation for the live sessions, we encourage participants to:

  1. explore the materials available

  2. Take a look at virtual training 2 ("From sequencer to polished reads for bacteria"), if you are not familiar with raw-data QC

  3. Suggest topics of interest for future virtual trainings

  
  

  • ForumAnnouncements
  • PageVirtual training organisation credits
• Collapse allExpand all
  Aim and Objectives

  Aim and Objectives

  Aim

  The aim of this virtual training workshop is to introduce the participants to theoretical and practical aspects of generating bacterial genome assemblies, and the common tools for how to assess assembly quality.

  
  

  Intended learning outcomes

  Upon completion of this workshop, participants will be able to:

  1.     Explain the basics of how raw sequencing reads are processed into genomes.

  2.     Explain why some organisms assemble into few contigs and others into a lot of contigs (when doing a de-novo assembly).

  3.     Describe the most common stats used for evaluating bacterial genome assemblies.

  4.     Understand the impact of read-length and base-calling quality for assembly.

  5.     Identify a contaminated genome assembly.

  6.     Be familiar with the software tools and strategies used for evaluating bacterial genome assemblies. 
• Delivery

  Delivery

  Format

  This virtual training takes place over two sessions that will be held on 4 and 7 December 2023, 10:00-14:30.

  
  

  Outline

  Session 1: Introducing genome assembly strategies and common QC-stats.

  Session 2: Interpretation of genome assembly stats in practice, and outlook on more advanced QC methods.
  

  
  

  Prerequisites

  There are no prerequisites.
  
• Software requirements

  Software requirements

  None. 

  The practical aspects of this workshop can all be done online. Result-files will also be provided, so it is possible to follow the workshop as an observer, without running any software. The workshop will include live demos on how to use various software, but the main focus will be on understanding how to interpret the results.

  
  

  Since this is a virtual workshop, and participants are expected to be working on widely different computing platforms, we do not provide help on how to install software (or troubleshoot, when software doesn’t perform as expected). However, the training will involve "demos" on how to run various software from the command-line. 

  We expect to use the following tools (and possibly a few more):

  • SPAdes
  • Unicycler
  • barrnap
  • Bandage
  • QUAST
  • kraken
  • snippy
  • mummer
  • artemis

  
  

  We will use both Illumina and nanopore reads as input data. You can already find some of the data under "Session 1" (Sequencing data and result files). We will populate the folder further during the workshop

  
  
• Session 1 (4 December)

  Session 1 (4 December)

  Upon completion of this session, participants will be able to:

  1.     Explain the basics of how raw sequencing reads are processed into genomes.

  2.     Explain why some organisms assemble into few contigs and others into a lot of contigs (when doing a de-novo assembly).

  3.     Describe the most common stats used for evaluating bacterial genome assemblies.

  •  

     
    

  • FolderPresentations
  • FolderSequencing data and result files
  • FolderResources
  • URLGitHub - ablab/spades: SPAdes Genome Assembler
  • URLGitHub - rrwick/Unicycler: hybrid assembly pipeline for bacterial genomes
• Session 2 (7 December)

  Session 2 (7 December)

  After attending this session participants will be able to:
  

  1.     Understand the impact of read-length and base-calling quality for assembly.

  2.     Identify a contaminated genome assembly.

  3.     Be familiar with the software tools and strategies used for evaluating bacterial genome assemblies.

  • FolderPresentations
  •  

• Contacts

  Contacts

  For any questions regarding the this virtual training, please use the discussion forum.

  If you have questions about the GenEpi-BioTrain programme, please address ECDC.Microbiology@ecdc.europa.eu.

  If you have questions regarding other training initiatives please contact: Courses@ecdc.europa.eu.

  If you have technical issues please contact ECDC Front Office FrontOffice@ecdc.europa.eu.