1st generation sequencing, 2nd generation sequencing, optical mapping, Hi-C, linked reads. So many technologies that can be used for generating genome assemblies! This begs the questions – which combination of technologies is optimal for generating error-free or platinum quality genomes?
Just using 1st and 2nd generation sequencing has some serious limitations. Vertebrate Genome Project (VGP) scientists, who aim to generate near error-free reference genome assemblies of ~70,000 extant vertebrate species, found that genomes assembled using only Sanger or next-gen sequencing often lead to missing genes/parts of genes or sometimes incorrectly assembled genes. In addition, biologically meaningful repetitive regions were also not assembled correctly. This means that scientists have to spend even more time trying to determine the correct gene structure using other methodologies or sometimes unknowingly work with artifactual gene structures and sequences, leading to false conclusions about biology.
To overcome these limitations, VGP has been working with a variety of technologies to generate platinum quality near error-free genomes. They have tested a variety of sequencing and scaffolding solutions which include short and long read sequencing as well as linked reads, Bionano optical mapping and Hi-C for scaffolding. Listen to this webinar by Dr.Erich Jarvis, chair of the Vertebrate Genome Project to learn which technologies gave chromosome length scaffolds.