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:

orcid logoAnthony Bretaudeau avatar Anthony BretaudeauMarcella Sozzoni avatar Marcella SozzoniEnis Afgan avatar Enis Afganorcid logoTeresa Müller avatar Teresa Müllerorcid logoDelphine Lariviere avatar Delphine LariviereNiall Beard avatar Niall BeardBazante Sanders avatar Bazante SandersFabian Recktenwald avatar Fabian Recktenwaldorcid logoPolina Polunina avatar Polina PoluninaAnton Nekrutenko avatar Anton Nekrutenkoorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoBjörn Grüning avatar Björn GrüningBrandon Pickett avatar Brandon Pickettorcid logoHelena Rasche avatar Helena Rascheorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoSimon Gladman avatar Simon Gladmanorcid logoNicola Soranzo avatar Nicola SoranzoGrace Hall avatar Grace Hallorcid logoPaul Zierep avatar Paul Ziereporcid logoTom Brown avatar Tom Brownorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoVini Salazar avatar Vini Salazarorcid logoMiaomiao Zhou avatar Miaomiao ZhouGildas Le Corguillé avatar Gildas Le Corguilléorcid logoBérénice Batut avatar Bérénice Batutorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoAnna Syme avatar Anna Symeorcid logoNate Coraor avatar Nate Coraororcid logoLinelle Abueg avatar Linelle Abuegorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoSolenne Correard avatar Solenne Correardorcid logoCristóbal Gallardo avatar Cristóbal GallardoMatúš Kalaš avatar Matúš KalašMarius van den Beek avatar Marius van den BeekGiulio Formenti avatar Giulio Formentiorcid logoErwan Corre avatar Erwan Correorcid logoLaura Leroi avatar Laura Leroiorcid logoStéphanie Robin avatar Stéphanie RobinVerena Moosmann avatar Verena Moosmannorcid logoAlexandre Cormier avatar Alexandre CormierWilliam Durand avatar William Durandorcid logoMaria Doyle avatar Maria Doyle

Funding

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

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Melbourne Bioinformatics
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Avans
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ABRomics
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The University of Melbourne
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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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Australian BioCommons