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 logoDelphine Lariviere avatar Delphine Lariviereorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoBjörn Grüning avatar Björn Grüningorcid logoBérénice Batut avatar Bérénice Batutorcid logoNate Coraor avatar Nate Coraororcid logoLinelle Abueg avatar Linelle Abuegorcid logoErwan Corre avatar Erwan CorreMarcella Sozzoni avatar Marcella SozzoniGrace Hall avatar Grace Hallorcid logoSolenne Correard avatar Solenne Correardorcid logoPolina Polunina avatar Polina Poluninaorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoSimon Gladman avatar Simon GladmanVerena Moosmann avatar Verena Moosmannorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoHelena Rasche avatar Helena RascheGiulio Formenti avatar Giulio Formentiorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoPaul Zierep avatar Paul Ziereporcid logoDeepti Varshney avatar Deepti Varshneyorcid logoMaria Doyle avatar Maria Doyleorcid logoLaura Leroi avatar Laura Leroiorcid logoTom Brown avatar Tom BrownWilliam Durand avatar William Durandorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoTristan Reynolds avatar Tristan ReynoldsBazante Sanders avatar Bazante SandersAnton Nekrutenko avatar Anton Nekrutenkoorcid logoVini Salazar avatar Vini SalazarFabian Recktenwald avatar Fabian RecktenwaldNiall Beard avatar Niall Beardorcid logoTeresa Müller avatar Teresa Müllerorcid logoAlexandre Cormier avatar Alexandre CormierGildas Le Corguillé avatar Gildas Le CorguilléMatúš Kalaš avatar Matúš Kalašorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoAnna Syme avatar Anna SymeBrandon Pickett avatar Brandon Pickettorcid logoMiaomiao Zhou avatar Miaomiao Zhou

Funding

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