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
Quality and contamination control in bacterial isolate using Illumina MiSeq Data
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.

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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:

orcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoStéphanie Robin avatar Stéphanie RobinAva Hoffman avatar Ava HoffmanRobert Meller avatar Robert MellerDeepti Varshney avatar Deepti VarshneyElizabeth Humphries avatar Elizabeth Humphriesorcid logoBérénice Batut avatar Bérénice Batutorcid logoWolfgang Maier avatar Wolfgang MaierNatalie Kucher avatar Natalie Kucherorcid logoHelena Rasche avatar Helena Rascheorcid logoCameron Hyde avatar Cameron Hydeorcid logoErwan Corre avatar Erwan CorreFrederick Tan avatar Frederick Tanorcid logoColine Royaux avatar Coline Royauxorcid logoMaria Doyle avatar Maria DoyleEric Tvedte avatar Eric Tvedteorcid logoClea Siguret avatar Clea SiguretJoachim Wolff avatar Joachim WolffKatherine Cox avatar Katherine CoxCandace Savonen avatar Candace Savonenorcid logoLaura Leroi avatar Laura Leroi

Funding

These individuals or organisations provided funding support for the development of this resource

References