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[2023 Edition] Mycobacterium tuberculosis complex NGS made easy: data analysis step-by-step

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Practical Information

Dates
9-13 January 2023
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:

After the trainings all participants are expected to:


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

9 January 2023

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

9 January 2023

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

10 January 2023

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

11 January 2023

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)

12 January 2023

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)

13 January 2023

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.

Acknowledgements

This course was made possible thanks to the efforts of…

TB-CAPT PanACEA Seq&Treat FIND Swiss Tropical and Public Health institute Ospedale San Raffaele LINQ

TB-CAPT and PanACEA are part of the EDCTP2 programme supported by the European Union. EDCTP EU



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