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
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An Introduction to Genome Assembly
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An introduction to get started in genome assembly and annotation
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Deeper look into Genome Assembly algorithms
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Genome assembly and assembly QC - Introduction short version
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Short Read Assembly
These tutorials cover genome assembly using short reads
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
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| Assembly of metagenomic sequencing data | |||||
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De Bruijn Graph Assembly
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| 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 |
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| 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 |
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| 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.
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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:
Alexandre Cormier
Bazante Sanders
Stéphanie Robin
Saskia Hiltemann
Cristóbal Gallardo
Grace Hall
Fabian Recktenwald
Helena Rasche
Deepti Varshney
Laura Leroi
Marius van den Beek
Tom Brown
William Durand
Vini Salazar
Alex Ostrovsky
Polina Polunina
Anthony Bretaudeau
Delphine Lariviere
Matúš Kalaš
Nicola Soranzo
Bérénice Batut
Natalie Whitaker-Allen
Simon Gladman
Miaomiao Zhou
Paul Zierep
Erwan Corre
Anton Nekrutenko
Tristan Reynolds
Giulio Formenti
Maria Doyle
Linelle Abueg
Gildas Le Corguillé
Verena Moosmann
Nate Coraor
Wolfgang Maier
Solenne Correard
Niall Beard
Enis Afgan
Anna Syme
Marcella Sozzoni
Teresa Müller
Brandon Pickett
Romane LIBOUBAN
Björn Grüning
Funding
These individuals or organisations provided funding support for the development of this resource
