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
biodiversity
Chloroplast genome assembly
plants nanopore jbrowse1 biodiversity
De Bruijn Graph Assembly
Decontamination of a genome assembly
biodiversity
Deeper look into Genome Assembly algorithms
ERGA post-assembly QC
plants animals genome assembly QC biodiversity
Genome Assembly Quality Control
assembly quality control biodiversity
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 biodiversity
Large genome assembly and polishing
assembly polishing nanopore plants biodiversity
Making sense of a newly assembled genome
gmod prokaryote microgalaxy jbrowse1
Unicycler Assembly
prokaryote microgalaxy biodiversity
Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads
covid19 biodiversity
Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data
pacbio eukaryote VGP biodiversity
Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step
pacbio eukaryote VGP biodiversity

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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:

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

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

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ABRomics
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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.