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 logoMiaomiao Zhou avatar Miaomiao ZhouVerena Moosmann avatar Verena Moosmannorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoSimon Gladman avatar Simon GladmanGiulio Formenti avatar Giulio Formentiorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoHelena Rasche avatar Helena Rascheorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoRomane LIBOUBAN avatar Romane LIBOUBANorcid logoPaul Zierep avatar Paul Ziereporcid logoTeresa Müller avatar Teresa Müllerorcid logoTom Brown avatar Tom BrownAnton Nekrutenko avatar Anton NekrutenkoBrandon Pickett avatar Brandon Pickettorcid logoPolina Polunina avatar Polina PoluninaBazante Sanders avatar Bazante SandersMarcella Sozzoni avatar Marcella Sozzoniorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoAnna Syme avatar Anna Symeorcid logoVini Salazar avatar Vini Salazarorcid logoErwan Corre avatar Erwan CorreFabian Recktenwald avatar Fabian Recktenwaldorcid logoLinelle Abueg avatar Linelle Abuegorcid logoBjörn Grüning avatar Björn Grüningorcid logoSolenne Correard avatar Solenne Correardorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoSaskia Hiltemann avatar Saskia HiltemannMatúš Kalaš avatar Matúš Kalašorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoBérénice Batut avatar Bérénice Batutorcid logoLaura Leroi avatar Laura LeroiGrace Hall avatar Grace Hallorcid logoTristan Reynolds avatar Tristan Reynoldsorcid logoNate Coraor avatar Nate Coraor

Funding

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