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 logoNate Coraor avatar Nate Coraororcid logoDelphine Lariviere avatar Delphine LariviereWilliam Durand avatar William Durandorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoBérénice Batut avatar Bérénice Batutorcid logoDeepti Varshney avatar Deepti VarshneyGiulio Formenti avatar Giulio Formentiorcid logoMaria Doyle avatar Maria Doyleorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoVini Salazar avatar Vini Salazarorcid logoSaskia Hiltemann avatar Saskia HiltemannMatúš Kalaš avatar Matúš KalašGrace Hall avatar Grace HallMarius van den Beek avatar Marius van den BeekVerena Moosmann avatar Verena Moosmannorcid logoSimon Gladman avatar Simon GladmanAnton Nekrutenko avatar Anton Nekrutenkoorcid logoErwan Corre avatar Erwan Correorcid logoSolenne Correard avatar Solenne CorreardMarcella Sozzoni avatar Marcella Sozzoniorcid logoTeresa Müller avatar Teresa Müllerorcid logoLinelle Abueg avatar Linelle AbuegBrandon Pickett avatar Brandon Pickettorcid logoPolina Polunina avatar Polina Poluninaorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoBjörn Grüning avatar Björn GrüningBazante Sanders avatar Bazante SandersFabian Recktenwald avatar Fabian Recktenwaldorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoAnna Syme avatar Anna SymeGildas Le Corguillé avatar Gildas Le Corguilléorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoHelena Rasche avatar Helena Rascheorcid logoTom Brown avatar Tom BrownEnis Afgan avatar Enis AfganNiall Beard avatar Niall Beardorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoPaul Zierep avatar Paul Ziereporcid logoLaura Leroi avatar Laura Leroi

Funding

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

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Melbourne Bioinformatics
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The University of Melbourne
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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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Australian BioCommons