One Health

Recently added tutorials, slides, FAQs, and events in the one-health topic

gtn logo

๐ŸŽฅ Recording of Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

By: Wolfgang Maier

A 55M long recording is now available.

Published: 2024-09-27T00:00:00+00:00
Tags: variant-analysis, covid19, virology, one-health

๐ŸŽฅ Recording of Identification of AMR genes in an assembled bacterial genome

By: Saim Momin

A 26M long recording is now available.

Published: 2024-09-24T00:00:00+00:00
Tags: genome-annotation, gmod, illumina, amr, one-health, jbrowse1, microgalaxy

๐Ÿ“ฐ 4th Mycobacterium tuberculosis complex NGS made easy

Tuberculosis (TB) is a big killer in many countries of the world, particularly in those with low and middle income. Next-generation sequencing has been key in improving our understanding of drug resistance acquisition and of transmission of Mycobacterium tuberculosis. Yet, the need for expertise guiding NGS implementation in laboratories and the lack of bioinformatic expertise, are main obstacles hindering the implementation of NGS into TB programs.

Published: 2024-07-08T00:00:00+00:00
Tags: news, NGS, Tuberculosis, Drug-resistance, transmission, evolution, one-health

๐ŸŽฅ Recording of M. tuberculosis Variant Analysis

By: Peter van Heusden

A 1H17M long recording is now available.

Published: 2024-06-11T00:00:00+00:00
Tags: variant-analysis, prokaryote, one-health, microgalaxy, tuberculosis

๐Ÿ“… 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).

Published: 2024-06-03T09:32:41+00:00
Tags: event, one-health, tuberculosis, NGS, Galaxy, training

๐Ÿ›ค๏ธ Detection of AMR genes in bacterial genomes

This learning path aims to teach you the basic steps to detect and check Antimicrobial resistance (AMR) genes in bacterial genomes using Galaxy.

Published: 2024-01-23T16:20:06+00:00
Tags: learning-pathway, amr, bacteria, microgalaxy, one-health

๐Ÿ“š Identification of AMR genes in an assembled bacterial genome

By: Bazante Sanders, Bรฉrรฉnice Batut

Antimicrobial resistance (AMR) is a global phenomenon with no geographical or species boundaries, which poses an important threat to human, animal and environmental health. It is a complex and growing problem that compromises our ability to treat bacterial infections.

Published: 2024-01-23T16:20:06+00:00
Tags: genome-annotation, gmod, illumina, amr, one-health, jbrowse1, microgalaxy

๐Ÿ“š Pox virus genome analysis from tiled-amplicon sequencing data

By: Wolfgang Maier, Tomas Klingstrรถm

Pox viruses (Poxviridae) are a large family of viruses, and members of it have various vertebrate and arthropod species as their natural hosts. The most widely known species in the family are the now extinct variola virus from the genus orthopoxvirus as the cause of smallpox, and vaccinia virus, a related, likely horsepox virus, which served as the source for the smallpox vaccine that allowed eradication of that disease.

Published: 2023-05-15T10:22:16+00:00
Tags: variant-analysis, virology, one-health

๐ŸŽฅ Recording of Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

By: Wolfgang Maier

A 55M long recording is now available.

Published: 2023-05-10T00:00:00+00:00
Tags: variant-analysis, covid19, virology, one-health

๐Ÿ“š Avian influenza viral strain analysis from gene segment sequencing data

By: Wolfgang Maier

Of the four species of influenza viruses (Influenza A-D), Influenza A is the most virulent in human hosts and subtypes of it have been responsible for all historic flu pandemics.

Published: 2022-11-21T16:45:21+00:00
Tags: variant-analysis, virology, one-health

๐Ÿ“š Tree thinking for tuberculosis evolution and epidemiology

By: Christoph Stritt, Daniela Brites, Galo A. Goig

Published: 2022-03-16T10:37:17+00:00
Tags: evolution, prokaryote, one-health, phylogenetics, microgalaxy

๐Ÿ“š Identifying tuberculosis transmission links: from SNPs to transmission clusters

By: Galo A. Goig, Daniela Brites, Christoph Stritt

In a disease outbreak situation, to understand the dynamics and the size of the outbreak, it is essential to detect transmission clusters to distinguish likely outbreak cases from unrelated background cases. Such detection is nowadays often based on actual sequencing data that enables quantitative conclusions about differences between pathogen isolates.

Published: 2022-03-16T08:35:43+00:00
Tags: evolution, prokaryote, one-health, microgalaxy

๐ŸŽฅ Recording of Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

By: Wolfgang Maier

A 1H30M long recording is now available.

Published: 2021-08-09T00:00:00+00:00
Tags: variant-analysis, covid19, virology, one-health

๐Ÿ“š Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

By: Wolfgang Maier, Bรฉrรฉnice Batut

Sequence-based monitoring of global infectious disease crises, such as the COVID-19 pandemic, requires capacity to generate and analyze large volumes of sequencing data in near real time. These data have proven essential for surveilling the emergence and spread of new viral variants, and for understanding the evolutionary dynamics of the virus.

Published: 2021-06-30T06:20:05+00:00
Tags: variant-analysis, covid19, virology, one-health

๐ŸŽฅ Recording of From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis

By: Anton Nekrutenko

A 15M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: variant-analysis, covid19, virology, one-health

๐ŸŽฅ Recording of M. tuberculosis Variant Analysis

By: Peter van Heusden

A 40M long recording is now available.

Published: 2021-02-15T00:00:00+00:00
Tags: variant-analysis, prokaryote, one-health, microgalaxy, tuberculosis

๐Ÿ“š M. tuberculosis Variant Analysis

By: Peter van Heusden, Simon Gladman, Thoba Lose

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 worldโ€™s most deadly infectious disease. The publication of the genome of M. tuberculosis H37Rv in 1998 gave researchers a powerful new tool for understanding this pathogen. This genome has been revised since then, with the latest version being available

Published: 2020-07-25T20:58:54+00:00
Tags: variant-analysis, prokaryote, one-health, microgalaxy, tuberculosis

๐Ÿ“š From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis

The aim of this tutorial is twofold:

Published: 2020-06-24T15:38:29+00:00
Tags: variant-analysis, covid19, virology, one-health

๐Ÿ“š Virtual screening of the SARS-CoV-2 main protease with rxDock and pose scoring

By: Simon Bray

This tutorial provides a companion to the work performed in March 2020 by InformaticsMatters, the Diamond Light Source, and the European Galaxy Team to perform virtual screening on candidate ligands for the SARS-CoV-2 main protease (MPro). This work is described in our dedicated site.

Published: 2020-03-27T13:26:13+00:00
Tags: computational-chemistry, covid19, one-health