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:

Fabian Recktenwald avatar Fabian Recktenwaldorcid logoTristan Reynolds avatar Tristan ReynoldsMarcella Sozzoni avatar Marcella SozzoniWilliam Durand avatar William DurandNiall Beard avatar Niall Beardorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoSolenne Correard avatar Solenne Correardorcid logoMaria Doyle avatar Maria Doyleorcid logoTom Brown avatar Tom Brownorcid logoBjörn Grüning avatar Björn Grüningorcid logoLaura Leroi avatar Laura LeroiEnis Afgan avatar Enis Afganorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoDeepti Varshney avatar Deepti VarshneyGiulio Formenti avatar Giulio Formentiorcid logoSimon Gladman avatar Simon Gladmanorcid logoPolina Polunina avatar Polina Poluninaorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoLinelle Abueg avatar Linelle AbuegMatúš Kalaš avatar Matúš KalašVerena Moosmann avatar Verena Moosmannorcid logoErwan Corre avatar Erwan Correorcid logoBérénice Batut avatar Bérénice Batutorcid logoWolfgang Maier avatar Wolfgang MaierGrace Hall avatar Grace Hallorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoNate Coraor avatar Nate CoraorBrandon Pickett avatar Brandon Pickettorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoPaul Zierep avatar Paul ZierepGildas Le Corguillé avatar Gildas Le Corguilléorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoHelena Rasche avatar Helena Rascheorcid logoVini Salazar avatar Vini Salazarorcid logoTeresa Müller avatar Teresa MüllerMarius van den Beek avatar Marius van den BeekBazante Sanders avatar Bazante Sandersorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoAnna Syme avatar Anna SymeAnton Nekrutenko avatar Anton Nekrutenko

Funding

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

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Australian BioCommons
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Avans
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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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Melbourne Bioinformatics
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The University of Melbourne