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

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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

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Contributors

This material was contributed to by:

Anton Nekrutenko avatar Anton NekrutenkoNiall Beard avatar Niall BeardBrandon Pickett avatar Brandon Pickettorcid logoMaria Doyle avatar Maria DoyleGrace Hall avatar Grace Hallorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoWolfgang Maier avatar Wolfgang MaierWilliam Durand avatar William Durandorcid logoTom Brown avatar Tom BrownGildas Le Corguillé avatar Gildas Le Corguilléorcid logoHelena Rasche avatar Helena RascheMarcella Sozzoni avatar Marcella Sozzoniorcid logoLaura Leroi avatar Laura Leroiorcid logoLinelle Abueg avatar Linelle Abuegorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoAnna Syme avatar Anna Symeorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoErwan Corre avatar Erwan CorreMarius van den Beek avatar Marius van den Beekorcid logoSolenne Correard avatar Solenne Correardorcid logoVini Salazar avatar Vini SalazarVerena Moosmann avatar Verena Moosmannorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoBjörn Grüning avatar Björn GrüningMatúš Kalaš avatar Matúš Kalašorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoPaul Zierep avatar Paul ZierepEnis Afgan avatar Enis Afganorcid logoStéphanie Robin avatar Stéphanie RobinGiulio Formenti avatar Giulio Formentiorcid logoTeresa Müller avatar Teresa Müllerorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoPolina Polunina avatar Polina Poluninaorcid logoNate Coraor avatar Nate Coraororcid logoBérénice Batut avatar Bérénice Batutorcid logoMiaomiao Zhou avatar Miaomiao ZhouFabian Recktenwald avatar Fabian RecktenwaldBazante Sanders avatar Bazante Sandersorcid logoSimon Gladman avatar Simon Gladman

Funding

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

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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.
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ABRomics
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Avans
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Australian BioCommons
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Melbourne Bioinformatics
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The University of Melbourne