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.

Follow topic updates with our RSS Feed

Community Resources

Community Home Maintainer Home

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

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:

orcid logoVini Salazar avatar Vini SalazarGildas Le Corguillé avatar Gildas Le Corguilléorcid logoNate Coraor avatar Nate Coraororcid logoPaul Zierep avatar Paul ZierepMarcella Sozzoni avatar Marcella Sozzoniorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoTom Brown avatar Tom Brownorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoMarius van den Beek avatar Marius van den BeekEnis Afgan avatar Enis AfganVerena Moosmann avatar Verena Moosmannorcid logoNicola Soranzo avatar Nicola SoranzoBrandon Pickett avatar Brandon Pickettorcid logoHelena Rasche avatar Helena RascheNiall Beard avatar Niall Beardorcid logoErwan Corre avatar Erwan Correorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoSaim Momin avatar Saim Mominorcid logoDeepti Varshney avatar Deepti VarshneyGiulio Formenti avatar Giulio Formentiorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoSolenne Correard avatar Solenne Correardorcid logoLinelle Abueg avatar Linelle Abuegorcid logoBjörn Grüning avatar Björn Grüningorcid logoAnna Syme avatar Anna Symeorcid logoAlex Ostrovsky avatar Alex OstrovskyMatúš Kalaš avatar Matúš Kalašorcid logoRomane LIBOUBAN avatar Romane LIBOUBANAnton Nekrutenko avatar Anton NekrutenkoFabian Recktenwald avatar Fabian RecktenwaldWilliam Durand avatar William Durandorcid logoTristan Reynolds avatar Tristan ReynoldsGrace Hall avatar Grace HallBazante Sanders avatar Bazante SandersNatalie Whitaker-Allen avatar Natalie Whitaker-Allenorcid logoMaria Doyle avatar Maria Doyleorcid logoBérénice Batut avatar Bérénice Batutorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoPolina Polunina avatar Polina Poluninaorcid logoSimon Gladman avatar Simon Gladmanorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoTeresa Müller avatar Teresa Müllerorcid logoLaura Leroi avatar Laura Leroiorcid logoMiaomiao Zhou avatar Miaomiao Zhou

Funding

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

Logo
Australian BioCommons
Logo
Avans
Logo
Melbourne Bioinformatics
Logo
The University of Melbourne
Logo
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.
Logo
ABRomics