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

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

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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 logoSaskia Hiltemann avatar Saskia HiltemannBrandon Pickett avatar Brandon PickettMatúš Kalaš avatar Matúš Kalašorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoTristan Reynolds avatar Tristan ReynoldsGiulio Formenti avatar Giulio Formentiorcid logoPolina Polunina avatar Polina Poluninaorcid logoErwan Corre avatar Erwan Correorcid logoSimon Gladman avatar Simon Gladmanorcid logoAlexandre Cormier avatar Alexandre CormierAnton Nekrutenko avatar Anton Nekrutenkoorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoTom Brown avatar Tom Brownorcid logoBérénice Batut avatar Bérénice BatutBazante Sanders avatar Bazante Sandersorcid logoHelena Rasche avatar Helena Rascheorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoTeresa Müller avatar Teresa Müllerorcid logoLaura Leroi avatar Laura LeroiNiall Beard avatar Niall BeardMarius van den Beek avatar Marius van den BeekFabian Recktenwald avatar Fabian RecktenwaldGrace Hall avatar Grace HallWilliam Durand avatar William Durandorcid logoVini Salazar avatar Vini Salazarorcid logoAnna Syme avatar Anna Symeorcid logoSolenne Correard avatar Solenne Correardorcid logoNate Coraor avatar Nate Coraororcid logoMaria Doyle avatar Maria Doyleorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoPaul Zierep avatar Paul Ziereporcid logoRomane LIBOUBAN avatar Romane LIBOUBANEnis Afgan avatar Enis Afganorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoBjörn Grüning avatar Björn GrüningMarcella Sozzoni avatar Marcella Sozzoniorcid logoLinelle Abueg avatar Linelle AbuegGildas Le Corguillé avatar Gildas Le CorguilléVerena Moosmann avatar Verena Moosmannorcid logoStéphanie Robin avatar Stéphanie Robin

Funding

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

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Avans
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ABRomics
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The University of Melbourne
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Melbourne Bioinformatics
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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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Australian BioCommons