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

Frequently Asked Questions

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

Funding

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