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.
Requirements
Before diving into this topic, we recommend you to have a look at:
Material
You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.Introduction
Start here if you are new to genome assembly in Galaxy
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
|
An Introduction to Genome Assembly
|
|||||
|
An introduction to get started in genome assembly and annotation
|
|||||
|
Deeper look into Genome Assembly algorithms
|
|||||
|
Genome assembly and assembly QC - Introduction short version
|
Short Read Assembly
These tutorials cover genome assembly using short reads
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
| Assembly of metagenomic sequencing data | |||||
|
De Bruijn Graph Assembly
|
|||||
| Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data |
Hybrid Assembly using Short and Long Reads
These tutorials cover hybrid genome assembly using both short and long reads
Assembly using PacBio Reads
These tutorials cover genome assembly using PacBio reads
Cleaning Genome Assembly
These tutorials cover how to clean and decontaminate a genome assembly
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
| Decontamination of a genome assembly |
Assessing Genome Assembly Quality
These tutorials cover how to assess the quality of a genome assembly
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
| ERGA post-assembly QC | |||||
| Genome Assembly Quality Control | |||||
| Making sense of a newly assembled genome |
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.
Follow topic updates rss-feed with our RSS Feed
Community Resources
Community Home Maintainer HomeEditorial Board
This material is reviewed by our Editorial Board:
Delphine Lariviere
Tristan Reynolds
Anton Nekrutenko
Are you on the editorial board or want to help out with this topic? View the topic maintainer page for ways to improve this topic!
Contributors
This material was contributed to by:
Erwan Corre
Enis Afgan
Fabian Recktenwald
Polina Polunina
Cristóbal Gallardo
Anna Syme
Niall Beard
Verena Moosmann
Anthony Bretaudeau
Saskia Hiltemann
Alexandre Cormier
Delphine Lariviere
Grace Hall
Marius van den Beek
Miaomiao Zhou
Bérénice Batut
Natalie Whitaker-Allen
Vini Salazar
Deepti Varshney
Giulio Formenti
Anton Nekrutenko
Laura Leroi
Nicola Soranzo
Solenne Correard
Tom Brown
Nate Coraor
Gildas Le Corguillé
Tristan Reynolds
Wolfgang Maier
Teresa Müller
Alex Ostrovsky
Helena Rasche
Linelle Abueg
Marcella Sozzoni
William Durand
Matúš Kalaš
Simon Gladman
Bazante Sanders
Paul Zierep
Stéphanie Robin
Björn Grüning
Brandon Pickett
Romane LIBOUBAN
Maria Doyle
Funding
These individuals or organisations provided funding support for the development of this resource
