Assembly

Learn all about Genome assembly. Start with the tutorial at your own pace. If you need support contact us via the Slack Channel gta_assembly.

Organisers(s) orcid logoDelphine Lariviere avatar Delphine Lariviere
Instructor(s) orcid logoAnna Syme avatar Anna Symeorcid logoBjörn Grüning avatar Björn Grüningorcid logoClea Siguret avatar Clea Siguretorcid logoDelphine Lariviere avatar Delphine LariviereGareth Price avatar Gareth PriceIgor Makunin avatar Igor MakuninMichael Schatz avatar Michael Schatzorcid logoSaim Momin avatar Saim MominNguyen Vo Minh Trung avatar Nguyen Vo Minh Trung

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Open Slack support channel for this track:   #gta_assembly

Introduction

In this section, we will introduce what is a genome assembly, how it works, and the metrics to evaluate the quality of an assembly.

Lesson Slides Hands-on Recordings

Introduction To Genome Assembly

Lecture Video (Slides)
ERGA post-assembly QC
plants animals genome assembly QC

Genome Assembly

In this section, we will present genome assemblies for different types of organisms.

Lesson Slides Hands-on Recordings
Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data
illumina assembly microgalaxy
Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data
pacbio eukaryote VGP
Assembly of metagenomic sequencing data
assembly metagenomics microgalaxy

Non-nuclear genome assembly

When sequencing organisms with non-nuclear DNA, the data contain sequencing for both nuclear and non-nuclear DNA. In this section we will learn how to assemble organelles genome.

Lesson Slides Hands-on Recordings
Assembly of the mitochondrial genome from PacBio HiFi reads
Chloroplast genome assembly
plants nanopore jbrowse1

Assembly decontamination

In this section we will learn how remove sequences that do not belong to the organism you want to sequence.

Lesson Slides Hands-on Recordings
Decontamination of a genome assembly