Mycobacterium tuberculosis complex NGS made easy
Virtual course
These series of webinars and tutorials aim at improving basic and applied knowledge associated with next-generation sequencing (NGS) technologies and their applications in the field of Tuberculosis (TB).
These series of webinars and tutorials aim at improving basic and applied knowledge associated with next-generation sequencing (NGS) technologies and their applications in the field of Tuberculosis (TB).
The trainings will introduce scalable and reproducible data analysis with Galaxy of Mycobacterium tuberculosis complex (MTBC) genomes.
A series of pre-recorded sessions and hands-on tutorials will show:
- How to differentiate sequencing technologies and which ones are most commonly applied in TB and how (Day 1)
- How NGS can be implement into TB laboratories (Day 1)
- How to do mapping and variant calling (Day 2)
- How to detect drug resistance conferring mutations, build phylogenetic trees and infer tuberculosis transmission (Day 3)
- How to use different web tools dedicated to targeted analysis and what it takes to do bioinformatics (Day 4).
After the trainings all participants are expected to:
- Describe how NGS is being used in TB research and clinical pratice
- Extract MTBC genomic variants from short sequencing reads
- Identify drug resistant mutations
- Identify genetic relationships and interpret a phylogenetic trees
- Use web applications designed for M. tuberculosis
Communication
- Chat on Slack channel #event-mtb-ngs (see “Setup” for instructions)
- Scheduled Questions & Answer sessions (Q&A) on Zoom
- Check your time correspondence with this time zone converter
A Slack channel will allow participants to communicate in real-time via chat. The channel should be used to troubleshoot and to get to know each other. There will be scheduled zoom sessions (Q&A) every day where you can meet the experts, discuss and ask questions (check the program to know the time and be aware of the difference in time zone). If you are in Asia you can attend the zoom sessions in the morning, if you are in America you can attend the sessions in the afternoon, no need to be there all the time.
Certificates
Requirements for acquiring a certificate:
- Being registered in the training
- Join us on Slack! (see “Setup” for instructions)
- Answer the assessments of days 1,2 and 3
- Fill the Feedback Survey
- As you finish the hands-on tutorials share your Galaxy history with us. See how to do this here and copy the url link in this table
Start the Course
On the day of the course, just go to the Program tab and follow the instructions! Make sure to follow the Setup instructions before starting!
Who is this course for?
Open for all, but target audience is clinicians and researchers using MTBC sequencing data.Organisers & Instructors
This event is brought to you by:
Before you start
Before starting the course, make sure to follow the setup instructions
Start the Course
There were unusually high rates of TB cases in your country this year. To characterize the underlying bacterial strains driving the epidemic, isolates have been sent for whole-genome sequencing. Doctors and public health authorities request information in order to take decisions. In this course it will be demonstrated how you would make use of NGS to answer several questions relevant for patient and public health system management such as:
- Are there cases of drug resistant bacteria?
- Is there transmission of drug resistance?
- Is there evidence of de novo emergence of resistance?
- Are there multiple infections per patient?
- Do we have on-going transmission?
We hope that at the end of the different training sessions you can answer this question on your own and can apply what you have learnt to your own data!
Day 1: Overview of NGS technologies & TB specific NGS solutions
Please watch the following pre-recorded webinars to know more about how NGS is being applied to TB and to know about what the WHO recomendations.
| Title | Description | ||
|---|---|---|---|
| Icebreaker |
Introduce yourself on Slack and tell us one fun fact about yourself! Post your answer to the #event-mtb-ngs Please feel free to respond to each other here, this channel is for troubleshooting but also for getting to know each other! :) |
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| Time | Title | Description | ||
|---|---|---|---|---|
10:30-11:00 Central European Time |
Welcome & set up live session |
We present the team and give general guidance on the training content and the set up. Join us on Zoom |
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| Webinar: Overview of NGS technologies & TB specific NGS solutions |
Introduction to different sequencing technologiesand what applies best to what kind of problem. Watch webinar (1h) Assessement: Share your thoughts with us here |
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| Webinar: Implementation of NGS for TB- WHO documents and other considerations |
Summary of the recommendations and considerations available from the WHO documents on the use of NGS for TB. Watch webinar (1h) Assessement: Share your thoughts with us here |
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| Webinar: Updated WHO catalogue version 2 |
Description of main changes introduced in the second version of the WHO catalogue on mutations associated with drug resistance released in November 2023. Watch webinar (6 min) |
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| Webinar: WHO recommendations on targeted NGS (tNGS) |
Summary of the recommendations and considerations available from the WHO documents on the use of targeted NGS for TB Watch webinar (15 min) |
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| Time | Title | Description | ||
|---|---|---|---|---|
14:00-16:00 Central European Time |
Meet the experts: Q&A session |
We would like to hear your opinion on the following questions and promote discussion in this Q&A session. Please let us know your thoughts on one or more of the following questions in the shared notes (link below);
Also take the chance to ask us or write down in the shared notes other questions you might have. The completion of the assessments is a requirement for the certificate of attendance. |
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Optional webinars: These are produced outside this training by tbnet and Stop TB Partnership and FIND, but might be of interest to you.
Implementing tNGS for detection of drug-resistant TB in high burden countries
Day 2: Mapping and variant calling
The 20 strains isolated in your country have been sequenced with Illumina technology to obtain whole-genome sequences. In this part of the workshop you will learn how to analyse those sequences.
In a typical bioinformatic pipeline you would store your sequences in a computer server where all necessary software would be installed. This would be a server running the operating system LINUX, which is the most efficient way to run bioinformatics pipelines (more on this on Day 4). You will be running your analysis in a LINUX server from Galaxy, but instead of writing directly commands to execute operations in the server, you will be executing operations through a Galaxy graphical interface. This allows you to have access to a LINUX server and to run workflows without knowing LINUX. Importantly, for training purposes it also allows you to dedicate more attention in trying to understand what is being done in each of the steps without having to understand the programing behind. This being said, working directly on a LINUX cluster provides you always more flexibility, but if you don’t have access to one, Galaxy is a very good alternative for data analysis.
| Title | Description | ||
|---|---|---|---|
| Icebreaker |
Come say Hi in Slack! Let us know you are joining today and are getting started! Today’s icebreaker question:
Post your answers in #event-mtb-ngs on Slack! Please feel free to respond to each other here, this channel is for socializing and getting to know each other! :) |
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Session 1: Learning Galaxy
You will need to understand how to use Galaxy to run all the hands- on tutorials and therefore is highly recommended that you follow the next webinar and hands-on on Galaxy. The good thing about this is that once you know how it works, you can use it to run your own analysis with your own data.
| Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|
| A short introduction to Galaxy | |||
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Galaxy Basics for genomics
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Session 2: Mapping and Variant calling of short MTBC reads
Let us imagine that you have received the sequences of the 20 strains, the first step is to assess the quality of sequencing. Once we are sure that the sequencing worked well, we typically compare our sequencing results to a reference genome (re-sequencing approach) by using a bioinformatics procedure usually called mapping. After, we will identify the genomic variants in our sequences with respect to the reference genome, a bioinformatics procedure called, variant calling. Once we are certain of the variants we have identified, usually we are interested in determining to what genes they belong, to what pathways, or for instance if they are likely to disrupt protein function. This procedure is called annotation. Once we have gone through each of these steps we are ready to analyse drug resistant patterns, draw phylogenetic relationships or identify clusters of transmission of M. tuberculosis.
You are now ready for performing bioinformatic analysis in Galaxy. Before we start we would like you to watch a short video on how Illumina sequencing works. Following that video we have prepared a webinar on mapping and variant calling of Illumina applied to MTBC. After watching it you will be hopefully able to know; how a reference genome is chosen, why we typically ignore some regions of the MTBC genomes or what is the difference between a fixed and a variable SNP and why do we care about it (among other things).
| Title | Description | ||
|---|---|---|---|
| Video: Illumina sequencing |
Please watch this 5-minute video about the principles behind Illumina sequencing |
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| Webinar: Mapping and Variant calling |
Main bioinformatics steps involved in mapping and variant calling from Illumina short reads applied to MTBC. Watch Webinar (45 minutes) Assessment: Share your thoughts with us here The completion of the assessments is a requirement for the certificate of attendance. |
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| Time | Title | Description | ||
|---|---|---|---|---|
11:30-12:30 Central European Time |
Meet the experts: Q&A session |
Meet the experts! Join us on Zoom. |
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| Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|
| M. tuberculosis Variant Analysis |
| Time | Title | Description | ||
|---|---|---|---|---|
16:30-17:30 Central European Time |
Meet the experts: Q&A session |
Join us on Zoom. |
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Day 3: Evolutionary epidemiology: using phylogenetics to understand DR emergence and Mtb transmission
We are ready to analyse drug resistant patterns, draw phylogenetic relationships or identify recent transmission among the isolates we have sampled in our population. Before delving into the analysis of the genomes we would like to share with you some notions important to the inference of direct transmission and to the interpretation of drug resistant patterns.
Evolutionary epidemiology: using phylogenetics to understand DR emergence and Mtb transmission
| Title | Description | ||
|---|---|---|---|
| Icebreaker |
Come say Hi in Slack! Let us know you are joining today and are getting started! Today’s icebreaker question:
Post your answers in #event-mtb-ngs on Slack! Please feel free to respond to each other here, this channel is for socializing and getting to know each other! :) |
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| Webinar: Drug resistance prediction |
Principles of drug resistance detection from genomic data Watch Webinar (20 minutes) Assessment: Share your thoughts with us here The completion of the assessments is a requirement for the certificate of attendance. |
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| Webinar: “Phylogenetic” mutations |
This video will introduce one special type of mutations to take into account when studying drug resistance patterns Watch Webinar (15 minutes) Assessment: Share your thoughts with us here The completion of the assessments is a requirement for the certificate of attendance. |
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| Webinar: The concept of clustering |
Main aspects of clustering analysis to infer transmission in MTBC Watch Webinar (15 minutes) |
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| Webinar: Genetic distance thresholds |
Clustering as an approximation to infer transmission Watch Webinar (15 minutes) Assessement: Share your thoughts with us here The completion of the assessment is a requirement for the certificate of attendance. |
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| Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|
| Identifying tuberculosis transmission links: from SNPs to transmission clusters |
| Time | Title | Description | ||
|---|---|---|---|---|
11:30-12:30 Central European time |
Meet the experts: Q&A session |
Discussion with the experts! Join us on Zoom. |
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| Hands-on:Introduction to phylogenetics |
Recommended tutorial from EMBL-EBI for those who want to learn more about phylogenetics. |
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| Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|
| Tree thinking for tuberculosis evolution and epidemiology |
| Title | Description | ||
|---|---|---|---|
| Check what you have learnt! |
We hope that you are enjoying the training, and that many things that you are learning will be useful for your research! We would like you to answer some questions, so both you and us, can assess whether the main concepts covered in the hands-on tutorials on Mtb NGS data analysis were understood. For that please follow the link bellow. If you are interested in knowing what we think about these questions join us on Day 5 The completion of the assessment is a requirement for the certificate of attendance. |
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| Time | Title | Description | ||
|---|---|---|---|---|
16:30-17:30 Central European Time |
Meet the experts: Q&A session |
Discussion with the experts! Join us on Zoom. |
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Day 4: Webtools dedicated to MTBC bioinformatics & Be a bioinformatician in the jungle (optional)
Session 1: Webtools dedicated to MTBC bioinformatics
The use of whole-genome sequencing (WGS) for antibiotic resistance prediction and routine typing of bacterial isolates has increased substantially in recent years. To date a multitude of solutions for analyzing WGS data of the Mycobacterium tuberculosis complex (MTBC) data have been developed. In the first part of the 4th day of this workshop, we introduce some freely available webtools and open source pipelines designed to analyze MTBC sequence data and we’ll provide some examples of how these tools work and how to interpret the results.
| Title | Description | ||
|---|---|---|---|
| Icebreaker |
Come say Hi in Slack! Let us know you are joining today and are getting started! Today’s icebreaker question:
Post your answers in #event-mtb-ngs on Slack! Please feel free to respond to each other here, this channel is for socializing and getting to know each other! :) |
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| Webinar: Use of web-tools & software for MTBC sequence analysis |
Introduction to most common web tools for fast identification of bacterial species from raw sequencing reads. Watch Webinar (50 minutes) Assessment: Share your thoughts with us here |
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| Webinar: Brief overview of MTBseq and MAGMA pipelines |
MAGMA and MTBseq pipelines are automated pipelines for mapping, variant calling and detection of resistance mediating and phylogenetic variants from whole genome sequence data of MTBC. This webinar presents the most important features between them. Watch Webinar (10 min) |
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| Time | Title | Description | ||
|---|---|---|---|---|
11:30-12:30 Central European Time |
Meet the experts: Q&A session |
Discussion with the experts! Join us on Zoom. |
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Session 2: Be a bioinformatician in the jungle (optional)
On Day 2 and 3 you have learned how you could use galaxy for analysing your own data. Establishing your own workflows in galaxy would allow you combining different tools and build your own pipeline without having to know how to program. If you are not so interested in having your own pipeline, webtools for WGS analysis can be very useful, as we have shown in the previous session.
However, in the last part of the training we would like to convey to you what it would take if would want to run Linux via the command line. The Linux operating system will be introduced, how to perform basic tasks using the Unix shell and how to install and run pipelines on the command line. You will learn the power of the Unix shell in performing complex and powerful tasks, often with just a few keystrokes or lines of code. In fact, Unix shell helps users automate repetitive tasks and easily combine smaller tasks into larger, more powerful workflows (i.e. pipelines). Use of the shell is fundamental to a wide range of advanced computing tasks, including high-performance computing. These webinars will introduce you to this powerful tool. Which approach to choose, Galaxy workflows, Webtools or native Linux depends on your needs, your interests and what computer resources you have available.
| Title | Description | ||
|---|---|---|---|
| Webinar: Introduction to Linux |
Introduction to Linux OS: installation and usage Watch Webinar (35 minutes) |
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| Webinar: How to run programs (Python, Docker, Nextflow) |
Learning how to install and use programs to analyze data Watch Webinar (35 minutes) |
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| Webinar: Demo on how to run the Linux command line |
Demo video on how to use the shell commands Watch Webinar (20 minutes) |
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| Hands-on: The Unix Shell |
Recommended tutorial from software carpentries to those wanting to learn Linux. View Carpentries Tutorial (4 hours) |
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| Time | Title | Description | ||
|---|---|---|---|---|
16:30-17:30 Central European time |
Meet the experts: Q&A session |
Join us on Zoom. If you have questions about web tools or what is the best way to become a bioinformatian, or if there are aspects of the webinars and tutorial that you would like to discuss in with the experts, please join the Q&A session. Fill free to write down in the shared notes those questions as well as that can help the experts to struture the discussion. |
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Day 5: Live Discussion
Today all experts will be available to answer your questions and discuss any of the tutorials, webinars, or questions related to your own data. Meet with us at the zoom link!
| Time | Lesson | Slides | Hands-on | Recordings |
|---|---|---|---|---|
10:00-12:30 Central European Time |
Meet the experts:Q&A session |
Discussion with the experts! Join us on Zoom. |
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Get set up for the course!
Follow the steps below to get set up with everything you need to participate in the course!
Create a Galaxy Account
Create an account on one of the following Galaxy servers:
You will get an email with activation link. It may end up in your junk folder.
Note: If you already have a Galaxy account you can skip this step and just log in to your existing account.
Join Galaxy Training Group (TIaaS)
Join TIaaS by clicking on the link below matching your Galaxy server:
This will give your analysis jobs priority on Galaxy for the duration of the event. Make sure you are logged in before clicking the link. You should see a green message box if all went well.
Join Slack!
We will provide support via Slack. Here you can ask any questions you may have during the course, and socialize with your fellow participants and instructors. The following steps will get you set up with Slack:
- Join Slack via this Invite Link
- Join the event channel: #event-mtb-ngs
- Introduce yourself here!
Instructor Zone
Check out our checklists for
- Organising a Workshop to check that you haven't forgotten any important step.
- Running a Workshop, helpful reminders closer to your event.
Request TIaaS
Training Infrastructure as a Service (TIaaS) is a service that allows you to request space for your course on a server, it helps ensure courses run smoothly by separating your trainee's jobs into a separate queue. Learn more about TIaaS in our tutorial.
The following links will open a (mostly) pre-filled out TIaaS form,
Once you receive a URL from the admins, please set it as a tiaas_link in your event metadata.
Add your event to the Galaxy Hub Event Horizon
To also list your event on the Galaxy Event Horizon, copy the text below, and add your event to the Galaxy Hub GitHub Repo. Create a folder for your event here, and add an index.md file with the following contents:
---
title: "Mycobacterium tuberculosis complex NGS made easy"
date: '2024-06-10'
days: 5
tease: These series of webinars and tutorials aim at improving basic and
applied knowledge associated with next-generation sequencing (NGS)
technologies and their applications in the field of Tuberculosis (TB).
#continent: EU
location: "Online"
external_url: "https://training.galaxyproject.org/training-material/events/2024-06-10-mtb-ngs.html"
gtn: true
contact: "d.brites@swisstph.ch"
subsites: [all]
---
Promote the Event
Tootable/Tweetable version:
Mycobacterium tuberculosis complex NGS made easy! 📢
These series of webinars and tutorials aim at improving basic and
applied knowledge associated with next-generation sequencing (NGS)
technologies and their applications in the field of Tuberculosis (TB).
📅 June 10 – 14, 2024
➡️ https://training.galaxyproject.org/training-material/events/2024-06-10-mtb-ngs.html
Slack-compatible version:
Mycobacterium tuberculosis complex NGS made easy! 📢
These series of webinars and tutorials aim at improving basic and
applied knowledge associated with next-generation sequencing (NGS)
technologies and their applications in the field of Tuberculosis (TB).
:calendar: June 10 – 14, 2024
:arrow_right: https://training.galaxyproject.org/training-material/events/2024-06-10-mtb-ngs.html
Version with schedule:
Mycobacterium tuberculosis complex NGS made easy! 📢
These series of webinars and tutorials aim at improving basic and
applied knowledge associated with next-generation sequencing (NGS)
technologies and their applications in the field of Tuberculosis (TB).
**Agenda**:
- Start the Course
- Day 1: Overview of NGS technologies & TB specific NGS solutions
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- Day 2: Mapping and variant calling
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- Day 3: Evolutionary epidemiology: using phylogenetics to understand DR emergence and Mtb transmission
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- Day 4: Webtools dedicated to MTBC bioinformatics & Be a bioinformatician in the jungle (optional)
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- Day 5: Live Discussion
📅 June 10 – 14, 2024
➡️ https://training.galaxyproject.org/training-material/events/2024-06-10-mtb-ngs.html
Event is Over
| event-date | June 10 – 14, 2024 |
| event-location | Online |
| event-cost | free |
| d.brites@swisstph.ch |
Add this event to your calendar Google Outlook Office 365
Organisers
Daniela Brites
Christoph Stritt
Andrea Cabibbe
Arash Ghodousi
Peter van Heusden
Liliana Rutaihwa
Andrea Spitaleri
Galo A. Goig
Instructors
Christoph Stritt
Daniela Brites
Andrea Cabibbe
Arash Ghodousi
Federico DiMarco
Peter van Heusden
Liliana Rutaihwa
Linzy Elton
Bethlehem Adnew
In collaboration with
Swiss Tropical and Public Health Institute
Università Vita-Salute San Raffaele
SANBI/UWC
PANGenS
IRCCS Ospedale San Raffaele
LINQ
FIND
PanACEA
EDCTP
EDCTP-EU
The European Union