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 using Oxford Nanopore MinION 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.

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:

Bazante Sanders avatar Bazante Sandersorcid logoAlexandre Cormier avatar Alexandre CormierLinelle Abueg avatar Linelle Abuegorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoSimon Gladman avatar Simon GladmanBrandon Pickett avatar Brandon PickettAvans Hogeschool avatar Avans HogeschoolFabian Recktenwald avatar Fabian Recktenwaldorcid logoStéphanie Robin avatar Stéphanie RobinMarcella Sozzoni avatar Marcella Sozzoniorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoHelena Rasche avatar Helena Rascheorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoAnna Syme avatar Anna Symeorcid logoLaura Leroi avatar Laura Leroiorcid logoWolfgang Maier avatar Wolfgang MaierGiulio Formenti avatar Giulio Formentiorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoErwan Corre avatar Erwan Correorcid logoBérénice Batut avatar Bérénice Batutorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoPolina Polunina avatar Polina PoluninaAnton Nekrutenko avatar Anton Nekrutenko

Funders

This material was funded by:

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