Assembly

DNA sequence data has become an indispensable tool for Molecular Biology & Evolutionary Biology. Study in these fields now require a genome sequence to work from. We call this a ‘Reference Sequence.’ We need to build a reference for each species. We do this by Genome Assembly. De novo Genome Assembly is the process of reconstructing the original DNA sequence from the fragment reads alone.

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
An Introduction to Genome Assembly
An introduction to get started in genome assembly and annotation
Assembly of metagenomic sequencing data
Chloroplast genome assembly
De Bruijn Graph Assembly
Deeper look into Genome Assembly algorithms
ERGA post-assembly QC
Genome Assembly Quality Control
Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data
Genome assembly using PacBio data
Large genome assembly and polishing
Making sense of a newly assembled genome
Unicycler Assembly
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads
VGP assembly pipeline - short version
VGP assembly pipeline: Step by Step

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/assembly-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 logoSimon Gladman avatar Simon GladmanAnton Nekrutenko avatar Anton Nekrutenkoorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoCristóbal Gallardo avatar Cristóbal Gallardo

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 logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoErwan Corre avatar Erwan Correorcid logoWolfgang Maier avatar Wolfgang MaierAnton Nekrutenko avatar Anton NekrutenkoLinelle Abueg avatar Linelle Abuegorcid logoPolina Polunina avatar Polina Poluninaorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoAnna Syme avatar Anna SymeMarcella Sozzoni avatar Marcella Sozzoniorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoBérénice Batut avatar Bérénice BatutBrandon Pickett avatar Brandon PickettGiulio Formenti avatar Giulio Formentiorcid logoHelena Rasche avatar Helena RascheBazante Sanders avatar Bazante Sandersorcid logoStéphanie Robin avatar Stéphanie RobinFabian Recktenwald avatar Fabian Recktenwaldorcid logoLaura Leroi avatar Laura LeroiAvans Hogeschool avatar Avans Hogeschoolorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoSimon Gladman avatar Simon Gladman

Funders

This material was funded by:

Gallantries: Bridging Training Communities in Life Science, Environment and Health avatar GallantriesABRomics avatar ABRomics