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 logoSimon Gladman avatar Simon Gladmanorcid logoSolenne Correard avatar Solenne CorreardBrandon Pickett avatar Brandon Pickettorcid logoTeresa Müller avatar Teresa Müllerorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoPolina Polunina avatar Polina Poluninaorcid logoTom Brown avatar Tom BrownNiall Beard avatar Niall Beardorcid logoAnna Syme avatar Anna SymeMarcella Sozzoni avatar Marcella SozzoniMatúš Kalaš avatar Matúš KalašFabian Recktenwald avatar Fabian Recktenwaldorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoBjörn Grüning avatar Björn Grüningorcid logoPaul Zierep avatar Paul Ziereporcid logoStéphanie Robin avatar Stéphanie Robinorcid logoSaskia Hiltemann avatar Saskia HiltemannAnton Nekrutenko avatar Anton Nekrutenkoorcid logoErwan Corre avatar Erwan CorreVerena Moosmann avatar Verena Moosmannorcid logoVini Salazar avatar Vini SalazarGildas Le Corguillé avatar Gildas Le CorguilléWilliam Durand avatar William Durandorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoNate Coraor avatar Nate Coraororcid logoLaura Leroi avatar Laura Leroiorcid logoCristóbal Gallardo avatar Cristóbal GallardoBazante Sanders avatar Bazante Sandersorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoLinelle Abueg avatar Linelle Abuegorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoMaria Doyle avatar Maria DoyleGiulio Formenti avatar Giulio Formentiorcid logoHelena Rasche avatar Helena RascheGrace Hall avatar Grace Hallorcid logoBérénice Batut avatar Bérénice Batut

Funding

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