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 (slides) and tutorial (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 of the mitochondrial genome from PacBio HiFi reads
Chloroplast genome assembly
De Bruijn Graph Assembly
Decontamination of a genome assembly
Deeper look into Genome Assembly algorithms
ERGA post-assembly QC
Genome Assembly Quality Control
Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data
Genome assembly and assembly QC - Introduction short version
Genome assembly using PacBio data
Hybrid genome assembly - Nanopore and Illumina
Large genome assembly and polishing
Making sense of a newly assembled genome
Unicycler Assembly
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads
Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data
Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step

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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 logoLaura Leroi avatar Laura LeroiVerena Moosmann avatar Verena MoosmannMatúš Kalaš avatar Matúš Kalašorcid logoSolenne Correard avatar Solenne Correardorcid logoHelena Rasche avatar Helena RascheFabian Recktenwald avatar Fabian Recktenwaldorcid logoVini Salazar avatar Vini Salazarorcid logoDeepti Varshney avatar Deepti VarshneyGiulio Formenti avatar Giulio Formentiorcid logoBérénice Batut avatar Bérénice BatutNiall Beard avatar Niall Beardorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoNate Coraor avatar Nate Coraororcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoSimon Gladman avatar Simon Gladmanorcid logoAnna Syme avatar Anna SymeMarcella Sozzoni avatar Marcella Sozzoniorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoErwan Corre avatar Erwan CorreBazante Sanders avatar Bazante Sandersorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoMaria Doyle avatar Maria Doyleorcid logoLinelle Abueg avatar Linelle Abuegorcid logoTeresa Müller avatar Teresa Müllerorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoPaul Zierep avatar Paul ZierepGrace Hall avatar Grace Hallorcid logoPolina Polunina avatar Polina Poluninaorcid logoWolfgang Maier avatar Wolfgang MaierAnton Nekrutenko avatar Anton Nekrutenkoorcid logoNicola Soranzo avatar Nicola SoranzoBrandon Pickett avatar Brandon Pickettorcid logoBjörn Grüning avatar Björn Grüningorcid logoStéphanie Robin avatar Stéphanie RobinWilliam Durand avatar William Durandorcid logoTom Brown avatar Tom Brownorcid logoDelphine Lariviere avatar Delphine LariviereGildas Le Corguillé avatar Gildas Le Corguillé

Funding

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