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