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

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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:

orcid logoSolenne Correard avatar Solenne Correardorcid logoLaura Leroi avatar Laura Leroiorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoErwan Corre avatar Erwan Correorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoBjörn Grüning avatar Björn Grüningorcid logoAnna Syme avatar Anna Symeorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoPolina Polunina avatar Polina Poluninaorcid logoSaskia Hiltemann avatar Saskia HiltemannFabian Recktenwald avatar Fabian RecktenwaldBazante Sanders avatar Bazante Sandersorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoTeresa Müller avatar Teresa Müllerorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoLinelle Abueg avatar Linelle Abuegorcid logoTom Brown avatar Tom BrownGrace Hall avatar Grace Hallorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoNate Coraor avatar Nate CoraorMarcella Sozzoni avatar Marcella Sozzoniorcid logoBérénice Batut avatar Bérénice Batutorcid logoSimon Gladman avatar Simon GladmanAnton Nekrutenko avatar Anton NekrutenkoMatúš Kalaš avatar Matúš Kalašorcid logoHelena Rasche avatar Helena RascheVerena Moosmann avatar Verena Moosmannorcid logoDeepti Varshney avatar Deepti VarshneyBrandon Pickett avatar Brandon PickettGiulio Formenti avatar Giulio Formentiorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoTristan Reynolds avatar Tristan Reynolds

Funding

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