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 logoAlexandre Cormier avatar Alexandre Cormierorcid logoSaskia Hiltemann avatar Saskia HiltemannMatúš Kalaš avatar Matúš Kalašorcid logoPaul Zierep avatar Paul Ziereporcid logoNate Coraor avatar Nate Coraororcid logoStéphanie Robin avatar Stéphanie Robinorcid logoVini Salazar avatar Vini Salazarorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoSimon Gladman avatar Simon Gladmanorcid logoDeepti Varshney avatar Deepti VarshneyBazante Sanders avatar Bazante Sandersorcid logoLinelle Abueg avatar Linelle Abuegorcid logoWolfgang Maier avatar Wolfgang MaierNiall Beard avatar Niall Beardorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoHelena Rasche avatar Helena Rascheorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoSolenne Correard avatar Solenne Correardorcid logoTeresa Müller avatar Teresa Müllerorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoAnna Syme avatar Anna SymeWilliam Durand avatar William Durandorcid logoBérénice Batut avatar Bérénice Batutorcid logoMaria Doyle avatar Maria DoyleGildas Le Corguillé avatar Gildas Le Corguilléorcid logoBjörn Grüning avatar Björn Grüningorcid logoTom Brown avatar Tom Brownorcid logoTristan Reynolds avatar Tristan ReynoldsGiulio Formenti avatar Giulio FormentiVerena Moosmann avatar Verena MoosmannAnton Nekrutenko avatar Anton Nekrutenkoorcid logoErwan Corre avatar Erwan Correorcid logoLaura Leroi avatar Laura Leroiorcid logoDelphine Lariviere avatar Delphine LariviereMarcella Sozzoni avatar Marcella SozzoniGrace Hall avatar Grace HallFabian Recktenwald avatar Fabian Recktenwaldorcid logoAnthony Bretaudeau avatar Anthony BretaudeauBrandon Pickett avatar Brandon Pickettorcid logoPolina Polunina avatar Polina Polunina

Funding

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