Sequence analysis

Analyses of sequences

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides () and tutorial () buttons below.

Requirements

Before diving into this topic, we recommend you to have a look at:

Material

Lesson Slides Hands-on Recordings Input dataset Workflows
Mapping
NCBI BLAST+ against the MAdLand
Quality Control
Removal of human reads from SARS-CoV-2 sequencing data
covid19
SARS-CoV-2 Viral Sample Alignment and Variant Visualization
covid19

Galaxy instances

You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.

You can also use the following Docker image for these tutorials:

docker run -p 8080:80 quay.io/galaxy/sequence-analysis-training

NOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.

It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

Editorial Board

This material is reviewed by our Editorial Board:

orcid logoAvatarYvan Le Brasorcid logoAvatarBérénice BatutAvatarJoachim Wolff

For any question related to this topic and the content, you can contact them or visit our Gitter channel.

Contributors

This material was contributed to by:

orcid logoAvatarMaria DoyleAvatarAva HoffmanAvatarFrederick Tanorcid logoAvatarBérénice Batutorcid logoAvatarAnthony BretaudeauAvatarDeepti Varshneyorcid logoAvatarAlexandre CormierAvatarJoachim WolffAvatarKatherine Coxorcid logoAvatarErwan Correorcid logoAvatarLaura LeroiAvatarElizabeth HumphriesAvatarCandace Savonenorcid logoAvatarStéphanie RobinAvatarNatalie Kucherorcid logoAvatarCameron Hydeorcid logoAvatarWolfgang Maierorcid logoAvatarHelena RascheAvatarRobert Meller

Funders

This material was funded by:

AvatarErasmus+ ProgrammeAvatarNational Human Genome Research Institute Genomic Data Science Community NetworkAvatarNational Human Genome Research Institute Genomic Data Science Analysis, Visualization, and Informatics Lab-Space

References