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

Funding

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