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:

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

Funding

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