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 logoSaskia Hiltemann avatar Saskia HiltemannMarius van den Beek avatar Marius van den Beekorcid logoBérénice Batut avatar Bérénice Batutorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoMaria Doyle avatar Maria Doyleorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoLinelle Abueg avatar Linelle AbuegBazante Sanders avatar Bazante SandersBrandon Pickett avatar Brandon Pickettorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoPolina Polunina avatar Polina PoluninaWilliam Durand avatar William Durandorcid logoVini Salazar avatar Vini SalazarAnton Nekrutenko avatar Anton Nekrutenkoorcid logoBjörn Grüning avatar Björn Grüningorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoAnna Syme avatar Anna Symeorcid logoNate Coraor avatar Nate CoraorFabian Recktenwald avatar Fabian RecktenwaldMatúš Kalaš avatar Matúš KalašGrace Hall avatar Grace Hallorcid logoSimon Gladman avatar Simon Gladmanorcid logoPaul Zierep avatar Paul ZierepEnis Afgan avatar Enis Afganorcid logoLaura Leroi avatar Laura LeroiGiulio Formenti avatar Giulio Formentiorcid logoNicola Soranzo avatar Nicola SoranzoMarcella Sozzoni avatar Marcella Sozzoniorcid logoSolenne Correard avatar Solenne Correardorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoTeresa Müller avatar Teresa Müllerorcid logoMiaomiao Zhou avatar Miaomiao ZhouGildas Le Corguillé avatar Gildas Le Corguilléorcid logoErwan Corre avatar Erwan CorreNiall Beard avatar Niall BeardVerena Moosmann avatar Verena Moosmannorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoHelena Rasche avatar Helena Rascheorcid logoTom Brown avatar Tom Brown

Funding

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

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