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:

William Durand avatar William Durandorcid logoLinelle Abueg avatar Linelle AbuegNiall Beard avatar Niall Beardorcid logoAnna Syme avatar Anna Symeorcid logoVini Salazar avatar Vini Salazarorcid logoTom Brown avatar Tom Brownorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoSaskia Hiltemann avatar Saskia HiltemannBazante Sanders avatar Bazante Sandersorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoBérénice Batut avatar Bérénice Batutorcid logoTeresa Müller avatar Teresa Müllerorcid logoMarius van den Beek avatar Marius van den Beekorcid logoNate Coraor avatar Nate CoraorGildas Le Corguillé avatar Gildas Le Corguilléorcid logoDeepti Varshney avatar Deepti VarshneyVerena Moosmann avatar Verena Moosmannorcid logoHelena Rasche avatar Helena RascheMarcella Sozzoni avatar Marcella Sozzoniorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoTristan Reynolds avatar Tristan ReynoldsBrandon Pickett avatar Brandon Pickettorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoLaura Leroi avatar Laura Leroiorcid logoErwan Corre avatar Erwan Correorcid logoSimon Gladman avatar Simon Gladmanorcid logoBjörn Grüning avatar Björn GrüningEnis Afgan avatar Enis AfganFabian Recktenwald avatar Fabian RecktenwaldAnton Nekrutenko avatar Anton Nekrutenkoorcid logoPolina Polunina avatar Polina PoluninaMatúš Kalaš avatar Matúš Kalašorcid logoCristóbal Gallardo avatar Cristóbal GallardoGiulio Formenti avatar Giulio FormentiGrace Hall avatar Grace Hallorcid logoMaria Doyle avatar Maria Doyleorcid logoSolenne Correard avatar Solenne Correardorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoPaul Zierep avatar Paul Ziereporcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoNicola Soranzo avatar Nicola Soranzo

Funding

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

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