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 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

Frequently Asked Questions

Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.

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Editorial Board

This material is reviewed by our Editorial Board:

orcid logoSimon Gladman avatar Simon Gladman Anton Nekrutenko avatar Anton Nekrutenko orcid logoDelphine Lariviere avatar Delphine Lariviere orcid logoCristóbal Gallardo avatar Cristóbal Gallardo

Contributors

This material was contributed to by:

Fabian Recktenwald avatar Fabian Recktenwald Niall Beard avatar Niall Beard orcid logoAnna Syme avatar Anna Syme Deepti Varshney avatar Deepti Varshney orcid logoLaura Leroi avatar Laura Leroi orcid logoErwan Corre avatar Erwan Corre Marius van den Beek avatar Marius van den Beek orcid logoAnthony Bretaudeau avatar Anthony Bretaudeau orcid logoBérénice Batut avatar Bérénice Batut Marcella Sozzoni avatar Marcella Sozzoni orcid logoStéphanie Robin avatar Stéphanie Robin orcid logoTom Brown avatar Tom Brown orcid logoNicola Soranzo avatar Nicola Soranzo orcid logoBjörn Grüning avatar Björn Grüning orcid logoSimon Gladman avatar Simon Gladman orcid logoPolina Polunina avatar Polina Polunina orcid logoMaria Doyle avatar Maria Doyle William Durand avatar William Durand orcid logoMiaomiao Zhou avatar Miaomiao Zhou Anton Nekrutenko avatar Anton Nekrutenko orcid logoLinelle Abueg avatar Linelle Abueg Teresa Müller avatar Teresa Müller orcid logoSaim Momin avatar Saim Momin Enis Afgan avatar Enis Afgan Matúš Kalaš avatar Matúš Kalaš orcid logoCristóbal Gallardo avatar Cristóbal Gallardo orcid logoDelphine Lariviere avatar Delphine Lariviere orcid logoAlexandre Cormier avatar Alexandre Cormier orcid logoHelena Rasche avatar Helena Rasche Gildas Le Corguillé avatar Gildas Le Corguillé orcid logoWolfgang Maier avatar Wolfgang Maier orcid logoNate Coraor avatar Nate Coraor orcid logoSaskia Hiltemann avatar Saskia Hiltemann Giulio Formenti avatar Giulio Formenti Brandon Pickett avatar Brandon Pickett orcid logoAlex Ostrovsky avatar Alex Ostrovsky Bazante Sanders avatar Bazante Sanders

Funding

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

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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.
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ABRomics