Education in the genomics era: Generating high-quality genome assemblies in university courses.

Axel Janke,Deepak K Gupta,Fritjof Lammers,Jordi De Raad,Magnus Wolf,Malte Petersen,Maria A Nilsson,Raphael T F Coimbra,Stefan Prost,Sven Winter,Tilman Schell

doi:10.1093/gigascience/giaa058

Abstract

Recent advances in genome sequencing technologies have simplified the generation of genome data and reduced the costs for genome assemblies, even for complex genomes like those of vertebrates. More practically oriented genomic courses can prepare university students for the increasing importance of genomic data used in biological and medical research. Low-cost third-generation sequencing technology, along with publicly available data, can be used to teach students how to process genomic data, assemble full chromosome-level genomes, and publish the results in peer-reviewed journals, or preprint servers. Here we outline experiences gained from 2 master's-level courses and discuss practical considerations for teaching hands-on genome assembly courses.

Highlights

The number of published genome assemblies has increased exponentially since the publication of the human genome in 2001 [1]
Recent advances in genome sequencing technologies have simplified the generation of genome data and reduced the costs for genome assemblies, even for complex genomes like those of vertebrates
An important step in this progression was the advent of “third-generation” sequencing with the release of Pacific Biosciences’ and Oxford Nanopore Technologies’ sequencing platforms. These technologies perform realtime sequencing of long, single DNA molecules and require no amplification to increase the sequencing detection signal strength [2]. The inclusion of these technologies has drastically improved the quality of generated genome assemblies and substantially decreased costs, enabling even small research groups to realise high-quality genome assemblies

Summary

Introduction

The number of published genome assemblies has increased exponentially since the publication of the human genome in 2001 [1]. Low-cost third-generation sequencing technology, along with publicly available data, can be used to teach students how to process genomic data, assemble full chromosome-level genomes, and publish the results in peer-reviewed journals, or preprint servers.

Results

Conclusion