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:

Marius van den Beek avatar Marius van den BeekGiulio Formenti avatar Giulio FormentiBrandon Pickett avatar Brandon Pickettorcid logoBjörn Grüning avatar Björn Grüningorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoDeepti Varshney avatar Deepti VarshneyBazante Sanders avatar Bazante Sandersorcid logoLinelle Abueg avatar Linelle Abuegorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoRomane LIBOUBAN avatar Romane LIBOUBANFabian Recktenwald avatar Fabian Recktenwaldorcid logoBérénice Batut avatar Bérénice BatutNiall Beard avatar Niall Beardorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoNate Coraor avatar Nate Coraororcid logoLaura Leroi avatar Laura Leroiorcid logoVini Salazar avatar Vini Salazarorcid logoTeresa Müller avatar Teresa Müllerorcid logoAlexandre Cormier avatar Alexandre CormierGildas Le Corguillé avatar Gildas Le Corguilléorcid logoErwan Corre avatar Erwan Correorcid logoMaria Doyle avatar Maria Doyleorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoHelena Rasche avatar Helena RascheAnton Nekrutenko avatar Anton NekrutenkoGrace Hall avatar Grace Hallorcid logoAlex Ostrovsky avatar Alex OstrovskyEnis Afgan avatar Enis Afganorcid logoSolenne Correard avatar Solenne CorreardVerena Moosmann avatar Verena Moosmannorcid logoAnna Syme avatar Anna Symeorcid logoPolina Polunina avatar Polina PoluninaMarcella Sozzoni avatar Marcella SozzoniMatúš Kalaš avatar Matúš Kalašorcid logoCristóbal Gallardo avatar Cristóbal GallardoWilliam Durand avatar William Durandorcid logoTom Brown avatar Tom Brownorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoSimon Gladman avatar Simon Gladmanorcid logoPaul Zierep avatar Paul Ziereporcid logoNicola Soranzo avatar Nicola Soranzo

Funding

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

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