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 logoSolenne Correard avatar Solenne Correardorcid logoAlex Ostrovsky avatar Alex OstrovskyBrandon Pickett avatar Brandon Pickettorcid logoHelena Rasche avatar Helena RascheGrace Hall avatar Grace Hallorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoBjörn Grüning avatar Björn GrüningGiulio Formenti avatar Giulio Formentiorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoErwan Corre avatar Erwan Correorcid logoMaria Doyle avatar Maria Doyleorcid logoNate Coraor avatar Nate Coraororcid logoPolina Polunina avatar Polina Poluninaorcid logoTeresa Müller avatar Teresa Müllerorcid logoLinelle Abueg avatar Linelle Abuegorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoBérénice Batut avatar Bérénice BatutVerena Moosmann avatar Verena Moosmannorcid logoAnna Syme avatar Anna Symeorcid logoVini Salazar avatar Vini Salazarorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoSimon Gladman avatar Simon Gladmanorcid logoTristan Reynolds avatar Tristan ReynoldsGildas Le Corguillé avatar Gildas Le CorguilléMarcella Sozzoni avatar Marcella SozzoniMatúš Kalaš avatar Matúš Kalašorcid logoDeepti Varshney avatar Deepti VarshneyBazante Sanders avatar Bazante Sandersorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoTom Brown avatar Tom Brownorcid logoNicola Soranzo avatar Nicola Soranzoorcid logoPaul Zierep avatar Paul Ziereporcid logoAnthony Bretaudeau avatar Anthony BretaudeauFabian Recktenwald avatar Fabian Recktenwaldorcid logoMiaomiao Zhou avatar Miaomiao ZhouNiall Beard avatar Niall Beardorcid logoDelphine Lariviere avatar Delphine LariviereAnton Nekrutenko avatar Anton NekrutenkoWilliam Durand avatar William Durandorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoLaura Leroi avatar Laura Leroi

Funding

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