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