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 () and 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 metagenomics microgalaxy
Assembly of the mitochondrial genome from PacBio HiFi reads
Chloroplast genome assembly
plants nanopore jbrowse1
De Bruijn Graph Assembly
Decontamination of a genome assembly
Deeper look into Genome Assembly algorithms
ERGA post-assembly QC
plants animals genome assembly QC
Genome Assembly Quality Control
assembly quality control
Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data)
nanopore assembly amr microgalaxy
Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data
illumina assembly microgalaxy
Genome assembly and assembly QC - Introduction short version
Genome assembly using PacBio data
assembly pacbio
Large genome assembly and polishing
assembly polishing nanopore plants
Making sense of a newly assembled genome
gmod prokaryote microgalaxy jbrowse1
Unicycler Assembly
prokaryote microgalaxy
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads
covid19
Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data
pacbio eukaryote VGP
Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
pacbio eukaryote VGP

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Editorial Board

This material is reviewed by our Editorial Board:

Anton Nekrutenko avatar Anton Nekrutenkoorcid logoDelphine Lariviere avatar Delphine Lariviere

Contributors

This material was contributed to by:

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

Funding

These individuals or organisations provided funding support for the development of this resource

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ABRomics
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Avans
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Gallantries
This project (2020-1-NL01-KA203-064717) is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.