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
Hybrid genome assembly - Nanopore and Illumina
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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Anton Nekrutenko avatar Anton Nekrutenkoorcid logoDelphine Lariviere avatar Delphine Lariviere

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Contributors

This material was contributed to by:

orcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoHelena Rasche avatar Helena Rascheorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoSimon Gladman avatar Simon Gladmanorcid logoErwan Corre avatar Erwan Correorcid logoLinelle Abueg avatar Linelle Abuegorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoLaura Leroi avatar Laura Leroiorcid logoTristan Reynolds avatar Tristan ReynoldsGrace Hall avatar Grace Hallorcid logoBérénice Batut avatar Bérénice Batutorcid logoPolina Polunina avatar Polina Poluninaorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoAnna Syme avatar Anna Symeorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoAnthony Bretaudeau avatar Anthony Bretaudeauorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoSolenne Correard avatar Solenne CorreardBazante Sanders avatar Bazante Sandersorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoCristóbal Gallardo avatar Cristóbal GallardoGiulio Formenti avatar Giulio Formentiorcid logoTeresa Müller avatar Teresa MüllerFabian Recktenwald avatar Fabian RecktenwaldMatúš Kalaš avatar Matúš KalašVerena Moosmann avatar Verena Moosmannorcid logoNate Coraor avatar Nate Coraororcid logoBjörn Grüning avatar Björn Grüningorcid logoRomane LIBOUBAN avatar Romane LIBOUBANMarcella Sozzoni avatar Marcella SozzoniAnton Nekrutenko avatar Anton NekrutenkoBrandon Pickett avatar Brandon Pickettorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoTom Brown avatar Tom Brown

Funding

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