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.
Lesson Slides Hands-on Recordings Input dataset Workflows
An Introduction to Genome Assembly
An introduction to get started in genome assembly and annotation
Assembly of metagenomic sequencing data
assembly metagenomics microgalaxy
Assembly of the mitochondrial genome from PacBio HiFi reads
biodiversity
Chloroplast genome assembly
plants nanopore jbrowse1 biodiversity
De Bruijn Graph Assembly
Decontamination of a genome assembly
biodiversity
Deeper look into Genome Assembly algorithms
ERGA post-assembly QC
plants animals genome assembly QC biodiversity
Genome Assembly Quality Control
assembly quality control biodiversity
Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
nanopore assembly amr microgalaxy
Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data
illumina assembly microgalaxy
Genome assembly and assembly QC - Introduction short version
Genome assembly using PacBio data
assembly pacbio biodiversity
Hybrid genome assembly - Nanopore and Illumina
assembly nanopore illumina denovo genomics
Large genome assembly and polishing
assembly polishing nanopore plants biodiversity
Making sense of a newly assembled genome
gmod prokaryote microgalaxy jbrowse1
Unicycler Assembly
prokaryote microgalaxy biodiversity
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads
covid19 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

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 logoMaria Doyle avatar Maria Doyleorcid logoBérénice Batut avatar Bérénice BatutBazante Sanders avatar Bazante Sandersorcid logoPaul Zierep avatar Paul Ziereporcid logoVini Salazar avatar Vini Salazarorcid logoLaura Leroi avatar Laura Leroiorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoSaskia Hiltemann avatar Saskia HiltemannFabian Recktenwald avatar Fabian Recktenwaldorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoSolenne Correard avatar Solenne Correardorcid logoNate Coraor avatar Nate Coraororcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoLinelle Abueg avatar Linelle Abuegorcid logoTom Brown avatar Tom Brownorcid logoAnna Syme avatar Anna SymeGrace Hall avatar Grace Hallorcid logoCristóbal Gallardo avatar Cristóbal GallardoGildas Le Corguillé avatar Gildas Le CorguilléMarius van den Beek avatar Marius van den Beekorcid logoMiaomiao Zhou avatar Miaomiao ZhouWilliam Durand avatar William DurandGiulio Formenti avatar Giulio Formentiorcid logoErwan Corre avatar Erwan Correorcid logoPolina Polunina avatar Polina Poluninaorcid logoDelphine Lariviere avatar Delphine LariviereBrandon Pickett avatar Brandon Pickettorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoBjörn Grüning avatar Björn Grüningorcid logoTeresa Müller avatar Teresa Müllerorcid logoSimon Gladman avatar Simon GladmanVerena Moosmann avatar Verena MoosmannMatúš Kalaš avatar Matúš KalašEnis Afgan avatar Enis AfganAnton Nekrutenko avatar Anton Nekrutenkoorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoNicola Soranzo avatar Nicola SoranzoNiall Beard avatar Niall BeardMarcella Sozzoni avatar Marcella Sozzoniorcid logoHelena Rasche avatar Helena Rasche

Funding

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

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