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:

Niall Beard avatar Niall Beardorcid logoAlexandre Cormier avatar Alexandre CormierGildas Le Corguillé avatar Gildas Le CorguilléFabian Recktenwald avatar Fabian Recktenwaldorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoMaria Doyle avatar Maria Doyleorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoTeresa Müller avatar Teresa Müllerorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoVini Salazar avatar Vini SalazarMatúš Kalaš avatar Matúš Kalašorcid logoPolina Polunina avatar Polina Poluninaorcid logoTom Brown avatar Tom BrownGrace Hall avatar Grace HallMarcella Sozzoni avatar Marcella Sozzoniorcid logoPaul Zierep avatar Paul Ziereporcid logoDeepti Varshney avatar Deepti Varshneyorcid logoLinelle Abueg avatar Linelle Abuegorcid logoHelena Rasche avatar Helena RascheBrandon Pickett avatar Brandon PickettGiulio Formenti avatar Giulio FormentiMarius van den Beek avatar Marius van den Beekorcid logoBérénice Batut avatar Bérénice BatutEnis Afgan avatar Enis Afganorcid logoErwan Corre avatar Erwan Correorcid logoMiaomiao Zhou avatar Miaomiao ZhouWilliam Durand avatar William Durandorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoWolfgang Maier avatar Wolfgang MaierBazante Sanders avatar Bazante Sandersorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoBjörn Grüning avatar Björn Grüningorcid logoLaura Leroi avatar Laura Leroiorcid logoSimon Gladman avatar Simon GladmanAnton Nekrutenko avatar Anton Nekrutenkoorcid logoAnna Syme avatar Anna SymeVerena Moosmann avatar Verena Moosmannorcid logoNate Coraor avatar Nate Coraororcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoSolenne Correard avatar Solenne Correard

Funding

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

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Australian BioCommons
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Melbourne Bioinformatics
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ABRomics
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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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Avans
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The University of Melbourne