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:
Bérénice Batut
Matúš Kalaš
Stéphanie Robin
Cristóbal Gallardo
Marius van den Beek
Natalie Whitaker-Allen
Nate Coraor
Giulio Formenti
Anna Syme
Linelle Abueg
Polina Polunina
Romane LIBOUBAN
Vini Salazar
Marcella Sozzoni
Anthony Bretaudeau
Delphine Lariviere
Brandon Pickett
Gildas Le Corguillé
Solenne Correard
Grace Hall
Teresa Müller
Alex Ostrovsky
Miaomiao Zhou
Enis Afgan
Deepti Varshney
Verena Moosmann
Tristan Reynolds
Niall Beard
Paul Zierep
Erwan Corre
Fabian Recktenwald
Saskia Hiltemann
Helena Rasche
Nicola Soranzo
Laura Leroi
Anton Nekrutenko
Alexandre Cormier
Tom Brown
Wolfgang Maier
William Durand
Simon Gladman
Björn Grüning
Maria Doyle
Bazante Sanders
Funding
These individuals or organisations provided funding support for the development of this resource
