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 () and 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
assembly metagenomics microgalaxy
De Bruijn Graph Assembly
Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data
illumina assembly microgalaxy

Hybrid Assembly using Short and Long Reads

These tutorials cover hybrid genome assembly using both short and long reads

Lesson Slides Hands-on Recordings Input dataset Workflows
Chloroplast genome assembly
plants nanopore jbrowse1 biodiversity
Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
nanopore assembly amr microgalaxy
Hybrid genome assembly - Nanopore and Illumina
assembly nanopore illumina denovo genomics
Large genome assembly and polishing
assembly polishing nanopore plants biodiversity
Unicycler Assembly
prokaryote microgalaxy biodiversity
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads
covid19 biodiversity

Assembly using PacBio Reads

These tutorials cover genome assembly using PacBio reads

Lesson Slides Hands-on Recordings Input dataset Workflows
Assembly of the mitochondrial genome from PacBio HiFi reads
biodiversity
Genome assembly using PacBio data
assembly pacbio biodiversity
Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data
pacbio eukaryote VGP biodiversity
Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
pacbio eukaryote VGP biodiversity

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
biodiversity

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
plants animals genome assembly QC biodiversity
Genome Assembly Quality Control
assembly quality control biodiversity
Making sense of a newly assembled genome
gmod prokaryote microgalaxy jbrowse1

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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Editorial Board

This material is reviewed by our Editorial Board:

orcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoTristan Reynolds avatar Tristan ReynoldsAnton Nekrutenko avatar Anton Nekrutenko

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Contributors

This material was contributed to by:

orcid logoDeepti Varshney avatar Deepti VarshneyVerena Moosmann avatar Verena Moosmannorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoMaria Doyle avatar Maria DoyleWilliam Durand avatar William Durandorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoAnthony Bretaudeau avatar Anthony BretaudeauFabian Recktenwald avatar Fabian RecktenwaldMatúš Kalaš avatar Matúš KalašBazante Sanders avatar Bazante Sandersorcid logoTom Brown avatar Tom BrownEnis Afgan avatar Enis Afganorcid logoAlexandre Cormier avatar Alexandre CormierGrace Hall avatar Grace Hallorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoTeresa Müller avatar Teresa Müllerorcid logoErwan Corre avatar Erwan Correorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoVini Salazar avatar Vini SalazarGildas Le Corguillé avatar Gildas Le Corguilléorcid logoWolfgang Maier avatar Wolfgang MaierMarcella Sozzoni avatar Marcella Sozzoniorcid logoNate Coraor avatar Nate Coraororcid logoHelena Rasche avatar Helena Rascheorcid logoLaura Leroi avatar Laura Leroiorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoSolenne Correard avatar Solenne Correardorcid logoPolina Polunina avatar Polina PoluninaGiulio Formenti avatar Giulio FormentiBrandon Pickett avatar Brandon Pickettorcid logoAlex Ostrovsky avatar Alex OstrovskyNiall Beard avatar Niall Beardorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoSimon Gladman avatar Simon Gladmanorcid logoAnna Syme avatar Anna SymeNatalie Whitaker-Allen avatar Natalie Whitaker-Allenorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoBjörn Grüning avatar Björn Grüningorcid logoMarius van den Beek avatar Marius van den Beekorcid logoBérénice Batut avatar Bérénice Batutorcid logoLinelle Abueg avatar Linelle Abuegorcid logoPaul Zierep avatar Paul ZierepAnton Nekrutenko avatar Anton Nekrutenko

Funding

These individuals or organisations provided funding support for the development of this resource

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Melbourne Bioinformatics
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Avans
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The University of Melbourne
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ABRomics
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Australian BioCommons
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Gallantries
This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.