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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Contributors

This material was contributed to by:

orcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoSolenne Correard avatar Solenne Correardorcid logoTeresa Müller avatar Teresa Müllerorcid logoErwan Corre avatar Erwan CorreBrandon Pickett avatar Brandon Pickettorcid logoRomane LIBOUBAN avatar Romane LIBOUBANVerena Moosmann avatar Verena Moosmannorcid logoBérénice Batut avatar Bérénice Batutorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoLaura Leroi avatar Laura Leroiorcid logoStéphanie Robin avatar Stéphanie RobinGiulio Formenti avatar Giulio Formentiorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoSimon Gladman avatar Simon Gladmanorcid logoAnna Syme avatar Anna Symeorcid logoHelena Rasche avatar Helena RascheFabian Recktenwald avatar Fabian Recktenwaldorcid logoCristóbal Gallardo avatar Cristóbal GallardoGrace Hall avatar Grace Hallorcid logoDeepti Varshney avatar Deepti VarshneyMarcella Sozzoni avatar Marcella Sozzoniorcid logoLinelle Abueg avatar Linelle Abuegorcid logoBjörn Grüning avatar Björn Grüningorcid logoPolina Polunina avatar Polina PoluninaBazante Sanders avatar Bazante Sandersorcid logoAlexandre Cormier avatar Alexandre CormierMatúš Kalaš avatar Matúš Kalašorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoTom Brown avatar Tom BrownAnton Nekrutenko avatar Anton Nekrutenkoorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoNate Coraor avatar Nate Coraor

Funding

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