Module: One Health
“One Health” is an integrated, unifying approach to balance and optimize the health of people, animals and the environment. It is particularly important to prevent, predict, detect, and respond to global health threats such as the COVID-19 pandemic.
The approach mobilizes multiple sectors, disciplines and communities at varying levels of society to work together. This way, new and better ideas are developed that address root causes and create long-term, sustainable solutions.
One Health involves the public health, veterinary and environmental sectors. One focus area of the One Health approach is the control of zoonoses (diseases that can spread between animals and humans), such as those caused by coronaviruses, influenza, pox viruses, or bacteria of the Mycobacterium tuberculosis complex.
Viral Pathogen Analysis
Demo Video
| Description: | A demo of SARS-CoV-2 sequencing data analysis from sequenced reads in NCBI’s SRA to called and annotated mutations for a batch of viral samples. |
| Length: | 15 minutes |
| Captions: | Anton Nekrutenko |
| Created: | 15 February 2021 |
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| Supported Servers: | Known Working Possibly Working |
Tutorial:
Avian influenza viral strain analysis from gene segment sequencing data
This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
| Tutorial: | Avian influenza viral strain analysis from gene segment sequencing data |
| Material: | GTN Tutorial |
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Instructor
Pox virus genome analysis from tiled-amplicon sequencing data
This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
| Tutorial: | Pox virus genome analysis from tiled-amplicon sequencing data |
| Material: | GTN Tutorial |
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Instructor
Tuberculosis Sequence Analysis
Webinar: Implementation of NGS for TB- WHO documents and other considerations
This webinar will summarize the recommendations and considerations available from the WHO documents on the use of NGS for TB
Note: This is a training session outside of the GTN. Please contact the authors if you have questions.
Variation in the genome of M. tuberculosis (Mtb) is associated with changes in phenotype, for example drug resistance and virulence. It is also useful for outbreak investigation as the single nucleotide polymorphisms (SNPs) in a sample can be used to build a phylogeny.
M. tuberculosis Variant Analysis (Lecture)
| Description: | Tuberculosis (TB) is an infectious disease caused by the bacterium Mycobacterium tuberculosis. According to the WHO, in 2018 there were 10.0 million new cases of TB worldwide and 1.4 million deaths due to the disease, making TB the world’s most deadly infectious disease. |
| Length: | 20 minutes |
| Captions: | Saskia Hiltemann |
| Created: | 15 February 2021 |
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M. tuberculosis Variant Analysis (Tutorial)
| Description: | Variation in the genome of M. tuberculosis (Mtb) is associated with changes in phenotype, for example drug resistance and virulence. It is also useful for outbreak investigation as the single nucleotide polymorphisms (SNPs) in a sample can be used to build a phylogeny. |
| Length: | 40 minutes |
| Captions: | Peter van Heusden, Nadia Goué, Helena Rasche |
| Created: | 15 February 2021 |
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Speaker
Identifying tuberculosis transmission links: from SNPs to transmission clusters
This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
| Tutorial: | Identifying tuberculosis transmission links: from SNPs to transmission clusters |
| Description: | Learning how to do clustering analysis and interpret drug resistance patterns |
| Material: | GTN Tutorial |
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Instructor
Tree thinking for tuberculosis evolution and epidemiology
This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
| Tutorial: | Tree thinking for tuberculosis evolution and epidemiology |
| Description: | Main principles of phylogenetic inference, tree interpretation |
| Material: | GTN Tutorial |
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Instructor
Building a pathogen surveillance system with Galaxy
Learn how to integrate Galaxy-based pathogen sequence data analysis into molecular surveillance programs
Tutorial Video
| Length: | 55 minutes |
| Captions: | Wolfgang Maier |
| Created: | 10 May 2023 |
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| Supported Servers: | Known Working |
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Tutorial Video
| Description: | This is a more technical tutorial which will teach you how to run workflows from the command line and scale your analyses. If you are on Windows, you will need WSL/WSL2 setup before this session. |
| Length: | 30 minutes |
| Captions: | Simon Bray |
| Created: | 15 February 2021 |
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| Supported Servers: | Known Working Possibly Working |
Removal of human reads from SARS-CoV-2 sequencing data
This is a self-study session. Please work through the materials on your own, and ask the instructors for help if you get stuck or have any questions!
| Tutorial: | Removal of human reads from SARS-CoV-2 sequencing data |
| Material: | GTN Tutorial |
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