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 logoLinelle Abueg avatar Linelle Abuegorcid logoPaul Zierep avatar Paul Ziereporcid logoDeepti Varshney avatar Deepti VarshneyMarcella Sozzoni avatar Marcella Sozzoniorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoTom Brown avatar Tom Brownorcid logoHelena Rasche avatar Helena RascheAnton Nekrutenko avatar Anton NekrutenkoVerena Moosmann avatar Verena MoosmannGrace Hall avatar Grace Hallorcid logoSimon Gladman avatar Simon Gladmanorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoBjörn Grüning avatar Björn GrüningMatúš Kalaš avatar Matúš Kalašorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoAlex Ostrovsky avatar Alex OstrovskyFabian Recktenwald avatar Fabian Recktenwaldorcid logoSolenne Correard avatar Solenne Correardorcid logoPolina Polunina avatar Polina Poluninaorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoTeresa Müller avatar Teresa Müllerorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoNate Coraor avatar Nate Coraororcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoVini Salazar avatar Vini SalazarGiulio Formenti avatar Giulio Formentiorcid logoLaura Leroi avatar Laura Leroiorcid logoStéphanie Robin avatar Stéphanie RobinBrandon Pickett avatar Brandon PickettBazante Sanders avatar Bazante Sandersorcid logoBérénice Batut avatar Bérénice Batutorcid logoAnna Syme avatar Anna Symeorcid logoErwan Corre avatar Erwan Correorcid logoMiaomiao Zhou avatar Miaomiao Zhou

Funding

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