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
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:

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Contributors

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Brandon Pickett avatar Brandon Pickettorcid logoTom Brown avatar Tom Brownorcid logoNate Coraor avatar Nate CoraorMatúš Kalaš avatar Matúš Kalašorcid logoLaura Leroi avatar Laura LeroiMarcella Sozzoni avatar Marcella Sozzoniorcid logoSimon Gladman avatar Simon Gladmanorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoBjörn Grüning avatar Björn Grüningorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoPolina Polunina avatar Polina Poluninaorcid logoSolenne Correard avatar Solenne Correardorcid logoLinelle Abueg avatar Linelle Abuegorcid logoHelena Rasche avatar Helena Rascheorcid logoTeresa Müller avatar Teresa MüllerAnton Nekrutenko avatar Anton NekrutenkoBazante Sanders avatar Bazante Sandersorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoErwan Corre avatar Erwan Correorcid logoBérénice Batut avatar Bérénice Batutorcid logoCristóbal Gallardo avatar Cristóbal GallardoGiulio Formenti avatar Giulio Formentiorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoRomane LIBOUBAN avatar Romane LIBOUBANFabian Recktenwald avatar Fabian Recktenwaldorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoAnna Syme avatar Anna Symeorcid logoStéphanie Robin avatar Stéphanie RobinVerena Moosmann avatar Verena Moosmann

Funding

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