Sequence analysis

Analyses of sequences

You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (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
Clean and manage Sanger sequences from raw files to aligned consensus
Mapping
NCBI BLAST+ against the MAdLand
Quality Control
Removal of human reads from SARS-CoV-2 sequencing data
SARS-CoV-2 Viral Sample Alignment and Variant Visualization
Screening assembled genomes for contamination using NCBI FCS

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 logoYvan Le Bras avatar Yvan Le Brasorcid logoBérénice Batut avatar Bérénice BatutJoachim Wolff avatar Joachim 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:

Katherine Cox avatar Katherine CoxFrederick Tan avatar Frederick Tanorcid logoCameron Hyde avatar Cameron Hydeorcid logoLaura Leroi avatar Laura Leroiorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoBérénice Batut avatar Bérénice BatutAva Hoffman avatar Ava Hoffmanorcid logoMaria Doyle avatar Maria Doyleorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoAnthony Bretaudeau avatar Anthony BretaudeauEric Tvedte avatar Eric Tvedteorcid logoAlexandre Cormier avatar Alexandre CormierElizabeth Humphries avatar Elizabeth HumphriesRobert Meller avatar Robert MellerNatalie Kucher avatar Natalie KucherCandace Savonen avatar Candace SavonenDeepti Varshney avatar Deepti Varshneyorcid logoColine Royaux avatar Coline RoyauxJoachim Wolff avatar Joachim Wolfforcid logoErwan Corre avatar Erwan Correorcid logoHelena Rasche avatar Helena Rasche

Funders

This material was funded by:

National Human Genome Research Institute Genomic Data Science Analysis, Visualization, and Informatics Lab-Space avatar NHGRI ANVILNational Human Genome Research Institute Genomic Data Science Community Network avatar NHGRI GDS Community NetworkNational Institutes of Health avatar NIHGallantries: Bridging Training Communities in Life Science, Environment and Health avatar Gallantries

References