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 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:

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

Contributors

This material was contributed to by:

orcid logoBérénice Batut avatar Bérénice Batutorcid logoTom Brown avatar Tom BrownMatúš Kalaš avatar Matúš Kalašorcid logoBjörn Grüning avatar Björn Grüningorcid logoErwan Corre avatar Erwan Correorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoNate Coraor avatar Nate Coraororcid logoAlex Ostrovsky avatar Alex OstrovskyTeresa Müller avatar Teresa MüllerBrandon Pickett avatar Brandon Pickettorcid logoHelena Rasche avatar Helena Rascheorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoAlexandre Cormier avatar Alexandre CormierAnton Nekrutenko avatar Anton Nekrutenkoorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoSimon Gladman avatar Simon Gladmanorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoStéphanie Robin avatar Stéphanie RobinMarcella Sozzoni avatar Marcella Sozzoniorcid logoLinelle Abueg avatar Linelle AbuegGiulio Formenti avatar Giulio FormentiDeepti Varshney avatar Deepti Varshneyorcid logoPolina Polunina avatar Polina Poluninaorcid logoSaskia Hiltemann avatar Saskia HiltemannFabian Recktenwald avatar Fabian Recktenwaldorcid logoAnna Syme avatar Anna Symeorcid logoLaura Leroi avatar Laura LeroiBazante Sanders avatar Bazante Sanders

Funding

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