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
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

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.

Follow topic updates rss-feed with our RSS Feed

Community Resources

Community Home Maintainer Home

Editorial Board

This material is reviewed by our Editorial Board:

Anton Nekrutenko avatar Anton Nekrutenkoorcid logoDelphine Lariviere avatar Delphine Lariviere

Are you on the editorial board or want to help out with this topic? View the topic maintainer page for ways to improve this topic!

Contributors

This material was contributed to by:

orcid logoLaura Leroi avatar Laura Leroiorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoTom Brown avatar Tom Brownorcid logoAlex Ostrovsky avatar Alex Ostrovskyorcid logoDeepti Varshney avatar Deepti Varshneyorcid logoRomane LIBOUBAN avatar Romane LIBOUBANMarcella Sozzoni avatar Marcella Sozzoniorcid logoErwan Corre avatar Erwan Correorcid logoPolina Polunina avatar Polina Poluninaorcid logoBérénice Batut avatar Bérénice BatutAnton Nekrutenko avatar Anton NekrutenkoBazante Sanders avatar Bazante Sandersorcid logoSolenne Correard avatar Solenne Correardorcid logoSimon Gladman avatar Simon Gladmanorcid logoNate Coraor avatar Nate Coraororcid logoWolfgang Maier avatar Wolfgang Maierorcid logoHelena Rasche avatar Helena Rascheorcid logoAnthony Bretaudeau avatar Anthony BretaudeauBrandon Pickett avatar Brandon Pickettorcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoAlexandre Cormier avatar Alexandre Cormierorcid logoAnna Syme avatar Anna Symeorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoTeresa Müller avatar Teresa MüllerVerena Moosmann avatar Verena MoosmannGiulio Formenti avatar Giulio FormentiMatúš Kalaš avatar Matúš Kalašorcid logoLinelle Abueg avatar Linelle Abuegorcid logoBjörn Grüning avatar Björn Grüningorcid logoMiaomiao Zhou avatar Miaomiao ZhouFabian Recktenwald avatar Fabian Recktenwald

Funding

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