Mycobacterium tuberculosis complex NGS made easy: data analysis step-by-step

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Practical Information

Dates: 21-25 March 2022
Location:: Online
Who:: Open for all, but target audience is clinicians and researchers using MTBC sequencing data.
Cost:: Free
Format:: Asynchronous; all training sessions are pre-recorded and provided in advance.
Support:: Live support in Slack (invite link, channel: #event-mtb-ngs), in which experts will answer questions on a peer-to-peer basis. Real-Time Q&A sessions See the schedule below to know when you can join us live! Zoom Link
Infastructure:: European Galaxy server and the Galaxy Training Material. Both will stay accessible and open after the training.
Organizer(s):: Daniela Brites
Supporting Institutions:: Swiss Tropical and Public Health Institute, IRCCS Ospedale San Raffaele, LINQ, FIND, Università Vita-Salute San Raffaele
Contact:: Daniela Brites

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Course Description

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

Program

This workshop is virtual and asynchronous. Training sessions are pre-recorded and the material provided in advance in the program below. Whenever you’re ready to get started, you can access the material by clicking in the respective days of the program. Everyday there are specific slots where you can meet the experts (check the schedule each day), ask questions and discuss ideas.

LET’S GET STARTED!

Start the Course!

Day 1 - WELCOME! And Practical Information

21 March 2022

Topic	Speaker	Time/Duration
Welcome and course information	All instructors	10:30-11:00am CET
Get ready for the course	-	5-10m

Day 1 - Overview of NGS technologies & TB specific NGS solutions

21 March 2022

Topic	Speaker	Description	Duration
Overview of NGS technologies & TB specific NGS solutions	Andrea Cabibbe	Webinar: This webinar will introduce different sequencing technologies and what applies best to what kind of problem.	1h10m
Implementation of NGS for TB- WHO documents and other considerations	Andrea Cabibbe	Webinar: This webinar will summarize the recommendations and considerations available from the WHO documents on the use of NGS for TB	1h
Live Discussion (14:00 -16:00 CET)	Andrea Cabibbe & Liliana Rutaihwa	Q&A session: How do I choose the right sequencing technology for my samples? What is needed for NGS? Why is NGS better for drug resistance and outbreak analysis?	2h

Day 2 - Mapping and variant calling

22 March 2022

Topic	Speaker	Description	Duration
A very short introduction to Galaxy	Anton Nekrutenko	Webinar: This video will introduce the Galaxy data analysis platform, and give a short demo on how to use it	10m
Galaxy 101	Anton Nekrutenko	Hands-on: This tutorial will introduce you to Galaxy. You will familiarize yourself with tools, workflows and histories. Those skills will be needed the next days	1h15m
Mapping and Variant calling	Daniela Brites	Video: llumina sequencing principles. Webinar: Main bioinformatics steps involved in mapping and variant calling from Illumina short reads applied to MTBC	45m
Live discussion (11:30-12:30 CET)	Daniela Brites & Galo Goig	Q&A session	1h
Mapping & Variant Calling	Peter van Heusden	Hands-on: Learn how to manipulate and process short reads obtained from MTBC isolates. Get familiar with quality control, mapping and NGS filetypes	2h
Live discussion (16:30-17:30 CET)	Daniela Brites & Galo Goig	Q&A Live session	1h

Day 3 - Evolutionary epidemiology: using phylogenetics to understand DR emergence and Mtb transmission

23 March 2022

Topic	Speaker	Description	Duration
Drug resistance prediction	Galo A. Goig	Webinar: This video will introduce principles of drug resistance detection from genomic data	20m
“Phylogenetic” mutations	Galo A. Goig	Webinar: This video will introduce one particular type of mutations to take into account when studying drug resistance patterns	15m
The concept of clustering	Galo A. Goig	Webinar: Main aspects of clustering analysis to infer transmission in MTBC	15m
Genetic distance thresholds	Galo A. Goig	Webinar: Clustering as an approximation to infer transmission	15m
Performing clustering analysis & drug resistance prediction	Galo A. Goig	Hands-on: Learning how to do clustering analysis and interpret drug resistance patterns	2h
Live discussion (11:30-12:30 CET)	Galo A. Goig & Christop Stritt	Q&A Live session	1h
Introduction to phylogenetics	EMBL-EBI	Recommended on-line introduction course from EMBL-EBI	1h
Inference of phylogenetic trees	Christoph Stritt	Hands-on: Main principles of phylogenetic inference, tree interpretation	1h
Live discussion (16:30-17:30 CET)	Christop Stritt & Galo A. Goig	Q&A Live session	1h

Day 4 - Webtools dedicated to MTBC bioinformatics & Be a bioinformatician in the jungle (optional)

24 March 2022

Topic	Speaker	Description	Duration
Web tools for analysis of MTBC sequenced data	Arash Ghodousi	Webinar: This video will introduce web tools designed for analysis of MTBC sequenced data	50m
Introduction to the MTBseq pipeline	Arash Ghodousi	Webinar: Introduction the MTBseq pipeline, an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants in MTBC	30m
Live discussion (11:30-12:30 CET)	Andrea Spitaleri	Q&A Live session	1h
Introduction to linux	Andrea Spitaleri	Webinar: Introduction to Linux OS: installation and usage	30m
How to run programs (Python, Docker, Nextflow)	Andrea Spitaleri	Webinar: Learning how to install and use programs to analyze data	30m
Demo video on how to use the shell commands	Andrea Spitaleri	Webinar: Demo video on how to use the shell commands	20m
The Unix Shell (optional)	Software carpentries	Recommended hands-on tutorial from software carpentries	4h
Live discussion (16:30-17:30 CET)	Andrea Spitaleri & Arash Ghodousi	Q&A Live session	1h

Day 5 - Live Discussion (optional)

25 March 2022

All instructors available live from 10:00h-12:30 am CET

Wrapping up

Please feel free to hang around in Slack and talk to us and the rest of the Galaxy community! Thanks for joining!!

After the Course

All these materials will remain online, so you can continue working on them for as long as you want. The only difference will be that you should ask your questions on the GTN Gitter channel, instead of Slack.