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 logoDelphine Lariviere avatar Delphine Lariviereorcid logoWolfgang Maier avatar Wolfgang MaierFabian Recktenwald avatar Fabian Recktenwaldorcid logoNate Coraor avatar Nate CoraorMatúš Kalaš avatar Matúš KalašGiulio Formenti avatar Giulio Formentiorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoAnna Syme avatar Anna Symeorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoBérénice Batut avatar Bérénice Batutorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoPaul Zierep avatar Paul Ziereporcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoMiaomiao Zhou avatar Miaomiao ZhouGrace Hall avatar Grace Hallorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoErwan Corre avatar Erwan Correorcid logoTeresa Müller avatar Teresa Müllerorcid logoTristan Reynolds avatar Tristan ReynoldsAnton Nekrutenko avatar Anton Nekrutenkoorcid logoHelena Rasche avatar Helena Rascheorcid logoSimon Gladman avatar Simon Gladmanorcid logoRomane LIBOUBAN avatar Romane LIBOUBANBrandon Pickett avatar Brandon Pickettorcid logoLaura Leroi avatar Laura LeroiBazante Sanders avatar Bazante Sandersorcid logoTom Brown avatar Tom Brownorcid logoPolina Polunina avatar Polina Poluninaorcid logoLinelle Abueg avatar Linelle AbuegVerena Moosmann avatar Verena Moosmannorcid logoSolenne Correard avatar Solenne Correardorcid logoBjörn Grüning avatar Björn GrüningMarcella Sozzoni avatar Marcella Sozzoni

Funding

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