New Tutorial: Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data

Author(s) orcid logoBérénice Batut avatar Bérénice Batutorcid logoWolfgang Maier avatar Wolfgang Maier
new tutorial variant-analysis covid-19

Posted on: 30 June 2021 PURL: https://gxy.io/GTN:N00019

Effectively monitoring 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 monitoring the emergence and spread of new variants, and for understanding the evolutionary dynamics of the virus.

The Galaxy community has developed high-quality analysis workflows to support

  • sensitive identification of SARS-CoV-2 allelic variants (AVs) starting with allele frequencies as low as 5% from deep sequencing reads
  • generation of user-friendly reports for batches of results
  • reliable and configurable consensus genome generation from called variants

The new tutorial “Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data” will teach you how to obtain, run and combine these workflows appropriately for different types of input data, be it:

  • Single-end data derived from Illumina-based RNAseq experiments
  • Paired-end data derived from Illumina-based RNAseq experiments
  • Paired-end data generated with Illumina-based Ampliconic (ARTIC) protocols, or
  • ONT FASTQ files generated with Oxford nanopore (ONT)-based Ampliconic (ARTIC) protocols

We would be happy to have your feedback or contributions for this new tutorial. That would help us improving it!

View Material
Analysis flow in the 'Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data' tutorial. It teaches how to obtain, run and combine workflows appropriately for 4 different types of input data. Image adapted from covid19.galaxyproject.org

Recent News

See all news

Learn to use MINERVA Platform's COVID-19 Disease Map with Galaxy

28 March 2024   by-covid pathways minerva gtn infrastructure new feature

As part of the work of BeYond COVID, we have developed a new integration between the MINERVA Platform’s COVID-19 Disease Map and Galaxy! Datasets created within Galaxy can now be seamlessly visualized in the MINERVA Platform, allowing you to explore your data in the context of the COVID-19 Disease Map.

Cool URLs Don't Change, GTN URLs don't either.

18 March 2024   gtn infrastructure new feature

At the Galaxy Training Network we are really committed to ensuring our training materials are Findable, Accessible, Interoperable, and Reusable. This means that we want to make sure that the URLs to our training materials are persistent and don’t change. The GTN wants you to be able to rely on our URLs once you’ve added them to a poster or training material, without having to worry about them breaking in the future.

Lost in a topic? Try a Learning Pathway!

4 March 2024   gtn infrastructure new feature

We know the GTN has a lot of learning materials (400 and counting!) which can make it quite difficult to figure out where to start in some topics.

GTN ❤️ GMOD

29 February 2024   new topic new feature genome annotation

Building upon the work previously done for the SARS-Cov-2 Topic we have further expanded the ‘tag based topics’ to support a new GMOD topic.