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 logoWolfgang Maier avatar Wolfgang Maierorcid logoTom Brown avatar Tom Brownorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoSaskia Hiltemann avatar Saskia HiltemannBazante Sanders avatar Bazante SandersBrandon Pickett avatar Brandon PickettMatúš Kalaš avatar Matúš Kalašorcid logoHelena Rasche avatar Helena Rascheorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoSolenne Correard avatar Solenne Correardorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoVini Salazar avatar Vini SalazarNiall Beard avatar Niall Beardorcid logoMaria Doyle avatar Maria Doyleorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoBjörn Grüning avatar Björn Grüningorcid logoPolina Polunina avatar Polina Poluninaorcid logoBérénice Batut avatar Bérénice Batutorcid logoAnna Syme avatar Anna Symeorcid logoSimon Gladman avatar Simon GladmanMarcella Sozzoni avatar Marcella Sozzoniorcid logoCristóbal Gallardo avatar Cristóbal GallardoAnton Nekrutenko avatar Anton Nekrutenkoorcid logoPaul Zierep avatar Paul Ziereporcid logoTristan Reynolds avatar Tristan ReynoldsFabian Recktenwald avatar Fabian RecktenwaldGiulio Formenti avatar Giulio Formentiorcid logoNate Coraor avatar Nate Coraororcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoLinelle Abueg avatar Linelle AbuegWilliam Durand avatar William Durandorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoLaura Leroi avatar Laura LeroiGildas Le Corguillé avatar Gildas Le CorguilléVerena Moosmann avatar Verena Moosmannorcid logoErwan Corre avatar Erwan Correorcid logoTeresa Müller avatar Teresa MüllerGrace Hall avatar Grace Hall

Funding

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