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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Anton Nekrutenko avatar Anton Nekrutenkoorcid logoDelphine Lariviere avatar Delphine Lariviere

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Contributors

This material was contributed to by:

Brandon Pickett avatar Brandon PickettMatúš Kalaš avatar Matúš Kalašorcid logoTom Brown avatar Tom Brownorcid logoHelena Rasche avatar Helena RascheMarcella Sozzoni avatar Marcella Sozzoniorcid logoBérénice Batut avatar Bérénice Batutorcid logoSolenne Correard avatar Solenne Correardorcid logoLinelle Abueg avatar Linelle AbuegFabian Recktenwald avatar Fabian RecktenwaldGiulio Formenti avatar Giulio FormentiBazante Sanders avatar Bazante SandersVerena Moosmann avatar Verena Moosmannorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoTeresa Müller avatar Teresa Müllerorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoErwan Corre avatar Erwan Correorcid logoBjörn Grüning avatar Björn Grüningorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoPolina Polunina avatar Polina Poluninaorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoAnna Syme avatar Anna SymeGrace Hall avatar Grace Hallorcid logoSimon Gladman avatar Simon Gladmanorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoNate Coraor avatar Nate Coraororcid logoLaura Leroi avatar Laura Leroiorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoSaskia Hiltemann avatar Saskia HiltemannAnton Nekrutenko avatar Anton Nekrutenkoorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoDelphine Lariviere avatar Delphine Lariviere

Funding

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