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:

Enis Afgan avatar Enis Afganorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoPolina Polunina avatar Polina Poluninaorcid logoVini Salazar avatar Vini Salazarorcid logoTom Brown avatar Tom Brownorcid logoBérénice Batut avatar Bérénice Batutorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoNate Coraor avatar Nate Coraororcid logoSimon Gladman avatar Simon Gladmanorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoSolenne Correard avatar Solenne Correardorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoAlexandre Cormier avatar Alexandre CormierFabian Recktenwald avatar Fabian RecktenwaldGrace Hall avatar Grace Hallorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoHelena Rasche avatar Helena RascheGildas Le Corguillé avatar Gildas Le Corguilléorcid logoAnna Syme avatar Anna Symeorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoMaria Doyle avatar Maria Doyleorcid logoLaura Leroi avatar Laura LeroiVerena Moosmann avatar Verena Moosmannorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoErwan Corre avatar Erwan Correorcid logoPaul Zierep avatar Paul ZierepBazante Sanders avatar Bazante SandersGiulio Formenti avatar Giulio Formentiorcid logoLinelle Abueg avatar Linelle AbuegMatúš Kalaš avatar Matúš Kalašorcid logoTeresa Müller avatar Teresa Müllerorcid logoWolfgang Maier avatar Wolfgang MaierMarcella Sozzoni avatar Marcella Sozzoniorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoAlex Ostrovsky avatar Alex OstrovskyNiall Beard avatar Niall Beardorcid logoDeepti Varshney avatar Deepti VarshneyWilliam Durand avatar William DurandBrandon Pickett avatar Brandon Pickettorcid logoBjörn Grüning avatar Björn GrüningAnton Nekrutenko avatar Anton NekrutenkoMarius van den Beek avatar Marius van den Beek

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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Australian BioCommons
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The University of Melbourne
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Melbourne Bioinformatics
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Avans