GenEpi-BioTrain - Virtual training 02: From sequencer to polished reads for bacteria

Topic outline

• From sequencer to polished reads for bacteria (GenEpi-BioTrain - Virtual training 2)

  From sequencer to polished reads for bacteria (GenEpi-BioTrain - Virtual training 2)

  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. Install the software indicated below

  3. Suggest topics of interest for future virtual trainings.

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

  Aim and Objectives

  Aim

  The aim of this virtual training is to introduce participants to the software tools commonly used for assessing quality and polishing Illumina and Nanopore bacterial sequence data. The participants will gain insights into interpreting quality control (QC) parameters as well as how to handle bad quality reads and contaminated data.

  Intended learning outcomes

  Upon Completion of the virtual course the participants should be able to:

  • Inspect the raw fastq files from the sequencer
  • Understand how sequences can differ based on the preparation methodology
  • Explain the differences between sequencing reads from Illumina and Nanopore
  • Assess the quality of sequence data and trim low quality data
  • Learn when to decontaminate and when to re-sequence
  • Generate an overview of the entire dataset using different tools
• Delivery

  Delivery

  Format

  This virtual training takes place over two sessions that will be held on 12 and 14 September 2023, 9:00-13:00.

  
  

  Outline

  Session 1: Introduction to and execution of QC assessment and contamination control.

  Session 2: Interpretation of QC and contamination results. Performing read trimming.
  

  
  

  Prerequisites

  The minimal prerequisites for participants to meet the learning objectives of this workshop are:

  • Ability to navigate a Unix terminal and use bioinformatic command line tools

  • Access to a Unix terminal (or emulator) during practical exercises

  For Windows users the following extra prerequisites are required:

  • Install and run a Unix emulator in windows (e.g., MobaXterm)
  • Install the required software stated under the "Software reqruiements" section.
    

  Participants not having these skills can still participate as observers.
• Software requirements

  Software requirements

  Prior to the training, participants are expected to download, install, and briefly test that the required software (listed below) can run in the terminal by enovking the help argument of each respective tool.

  ●      FastQC (Source page: FastQC)

  ●      MultiQC (Soruce page: https://github.com/ewels/MultiQC)

  ●      Nanoplot (Source page: https://github.com/wdecoster/NanoPlot)
  

  ●      Trimmomatic (Source page: http://www.usadellab.org/cms/?page=trimmomatic)

  ●      FiltLong (Source page: https://github.com/rrwick/Filtlong)

  ●      Chopper (Source page: https://github.com/wdecoster/chopper)

  
  

  Recommendation

  If on a Unix based OS (Not windows), consider installing miniconda following the official instructions: https://conda.io/projects/conda/en/latest/user-guide/install/index.html

  Aim for creating individual environments for each tool separately while installing them, as some tools may have conflicting software dependencies.
  

  Example:
  

  In order to install fastqc start out by searching and accessing the top search hit for "fastqc conda" on google (should be a page on the anaconda.org domain)

  Next in the terminal, create an environment for each of the packages and install the software. Start by executing the following command:

  conda env create -n fastqc
  

  Now copy the install code from the anaconda page found by googling the specific tool, before pressing enter, make sure to add -n fastqc
  to the end of the pasted command.
  

  conda install -c bioconda fastqc -n fastqc
  

  
  

  Repeat for all other tools, do mind to change the environment name (-n) and the channel (-c) according to the installation instructions for each respective tool.

  
  

  Whenever using a software, load its environment by running a:

  conda activate XYZ

  
  

  Changing the XYZ out with the name of the environment (the tool if following these instructions).

  For fastqc the environment can be activated by executing:

  conda activate fastq
  
• Session 1 (12 September): Introduction to and execution of QC assessment and contamination control

  Session 1 (12 September): Introduction to and execution of QC assessment and contamination control

  After attending this session participants will be able to:

  • Inspect the raw fastq files from the sequencer
  • Understand how sequences can differ based on the preparation methodology
  • Explain the differences between sequencing reads from Illumina and Nanopore

  • FileSeq2Preb-published
  • S1 - Select the checkbox to the right once you have completed watching the recorded session

     

     
    

  • FolderSequencing data
  • FilePart 1 - Illumina quality assessment
  • FilePart 2 - Nanopore quality control
• Session 2 (14 September): Interpretation of QC and contamination results. Performing read trimming

  Session 2 (14 September): Interpretation of QC and contamination results. Performing read trimming

  After attending this session participants will be able to:

  • Assess the quality of sequence data and trim low quality data
  • Learn when to decontaminate and when to re-sequence
  • Generate an overview of an entire dataset using different tools

  • FileSeq2Preb session2 published
  • S2 - Select the checkbox to the right once you have completed watching the recorded session

     

    
    

  • FileTrimmomatic
  • FileLong read trimming and filtering
  • FileMultiQC
• 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.