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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Editorial Board

This material is reviewed by our Editorial Board:

orcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoTristan Reynolds avatar Tristan ReynoldsAnton Nekrutenko avatar Anton Nekrutenko

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Contributors

This material was contributed to by:

orcid logoCristóbal Gallardo avatar Cristóbal Gallardoorcid logoVini Salazar avatar Vini Salazarorcid logoMiaomiao Zhou avatar Miaomiao Zhouorcid logoDelphine Lariviere avatar Delphine LariviereFabian Recktenwald avatar Fabian Recktenwaldorcid logoPolina Polunina avatar Polina PoluninaMarcella Sozzoni avatar Marcella Sozzoniorcid logoAnna Syme avatar Anna Symeorcid logoBjörn Grüning avatar Björn Grüningorcid logoPaul Zierep avatar Paul Ziereporcid logoTeresa Müller avatar Teresa Müllerorcid logoNate Coraor avatar Nate Coraororcid logoLinelle Abueg avatar Linelle Abuegorcid logoTom Brown avatar Tom Brownorcid logoAlex Ostrovsky avatar Alex OstrovskyAnton Nekrutenko avatar Anton Nekrutenkoorcid logoTristan Reynolds avatar Tristan ReynoldsGrace Hall avatar Grace Hallorcid logoStéphanie Robin avatar Stéphanie Robinorcid logoRomane LIBOUBAN avatar Romane LIBOUBANBazante Sanders avatar Bazante Sandersorcid logoDeepti Varshney avatar Deepti VarshneyVerena Moosmann avatar Verena Moosmannorcid logoLaura Leroi avatar Laura Leroiorcid logoBérénice Batut avatar Bérénice Batutorcid logoWolfgang Maier avatar Wolfgang Maierorcid logoAlexandre Cormier avatar Alexandre CormierGiulio Formenti avatar Giulio FormentiBrandon Pickett avatar Brandon Pickettorcid logoSimon Gladman avatar Simon Gladmanorcid logoHelena Rasche avatar Helena Rascheorcid logoSaskia Hiltemann avatar Saskia Hiltemannorcid logoErwan Corre avatar Erwan Correorcid logoSolenne Correard avatar Solenne Correardorcid logoAnthony Bretaudeau avatar Anthony BretaudeauMatúš Kalaš avatar Matúš Kalaš

Funding

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