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 logoWolfgang Maier avatar Wolfgang Maierorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoNate Coraor avatar Nate CoraorEnis Afgan avatar Enis Afganorcid logoSimon Gladman avatar Simon Gladmanorcid logoBérénice Batut avatar Bérénice Batutorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoHelena Rasche avatar Helena RascheAnton Nekrutenko avatar Anton Nekrutenkoorcid logoDeepti Varshney avatar Deepti VarshneyNiall Beard avatar Niall Beardorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoAnthony Bretaudeau avatar Anthony BretaudeauBazante Sanders avatar Bazante Sandersorcid logoPolina Polunina avatar Polina Poluninaorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoTeresa Müller avatar Teresa Müllerorcid logoErwan Corre avatar Erwan CorreMarius van den Beek avatar Marius van den BeekMatúš Kalaš avatar Matúš Kalašorcid logoLinelle Abueg avatar Linelle Abuegorcid logoMiaomiao Zhou avatar Miaomiao ZhouWilliam Durand avatar William DurandGrace Hall avatar Grace HallMarcella Sozzoni avatar Marcella SozzoniGildas Le Corguillé avatar Gildas Le CorguilléGiulio Formenti avatar Giulio Formentiorcid logoSolenne Correard avatar Solenne CorreardFabian Recktenwald avatar Fabian Recktenwaldorcid logoBjörn Grüning avatar Björn Grüningorcid logoMaria Doyle avatar Maria Doyleorcid logoAlexandre Cormier avatar Alexandre CormierBrandon Pickett avatar Brandon Pickettorcid logoVini Salazar avatar Vini Salazarorcid logoTom Brown avatar Tom Brownorcid logoPaul Zierep avatar Paul Ziereporcid logoLaura Leroi avatar Laura Leroiorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoAnna Syme avatar Anna SymeVerena Moosmann avatar Verena Moosmann

Funding

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

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The University of Melbourne
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Melbourne Bioinformatics
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Avans
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ABRomics
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Australian BioCommons
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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.