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:

Fabian Recktenwald avatar Fabian Recktenwaldorcid logoSimon Gladman avatar Simon Gladmanorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoLinelle Abueg avatar Linelle Abuegorcid logoVini Salazar avatar Vini Salazarorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoPolina Polunina avatar Polina PoluninaBazante Sanders avatar Bazante Sandersorcid logoNate Coraor avatar Nate Coraororcid logoPaul Zierep avatar Paul ZierepMatúš Kalaš avatar Matúš KalašAnton Nekrutenko avatar Anton NekrutenkoVerena Moosmann avatar Verena Moosmannorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoErwan Corre avatar Erwan Correorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoLaura Leroi avatar Laura Leroiorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoAnna Syme avatar Anna Symeorcid logoBjörn Grüning avatar Björn GrüningMarcella Sozzoni avatar Marcella Sozzoniorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoBérénice Batut avatar Bérénice Batutorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoSolenne Correard avatar Solenne Correardorcid logoTom Brown avatar Tom Brownorcid logoWolfgang Maier avatar Wolfgang MaierGiulio Formenti avatar Giulio Formentiorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoTeresa Müller avatar Teresa Müllerorcid logoHelena Rasche avatar Helena RascheBrandon Pickett avatar Brandon PickettGrace Hall avatar Grace Hall

Funding

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