Assembly

Learn all about Genome assembly.

Organisers(s) orcid logoDelphine Lariviere avatar Delphine Lariviere
Instructor(s) orcid logoDelphine Lariviere avatar Delphine Lariviereorcid logoSaim Momin avatar Saim Mominorcid logoBjörn Grüning avatar Björn Grüningorcid logoClea Siguret avatar Clea SiguretMichael Schatz avatar Michael SchatzGareth Price avatar Gareth Priceorcid logoAnna Syme avatar Anna SymeNguyen Vo Minh Trung avatar Nguyen Vo Minh TrungIgor Makunin avatar Igor Makunin

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
An introduction to get started in genome assembly and annotation
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

Mitochondrial Genome Assembly

Tutorial (will come soon)
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

Assembly decontamination

Tutorial (will come soon)