Last-gen nostalgia: a lighthearted rant and reflection on genome sequencing culture

David Roy Smith

doi:10.3389/fgene.2014.00146

Abstract

I sometimes see them in my dreams. The colorful peaks and troughs, the sharp, crisp waves spread across my computer screen, the rolling nitrogenous mountains, each with its own nucleotide sitting solidly on the summit. I'm talking about electropherograms, of course. Remember them? Those beautiful but oh so “old-gen” bioinformatics data generated from automated Sanger sequencing machines, such as the Applied Biosystems 370—the geriatric of genome sequencers. Don't laugh. It was these capillary-based electrophoretic technologies that gave us the draft human genome sequence (Lander et al., 2001) and the genome maps of many other model organisms, from the bacterium Haemophilus influenza to the yeast Saccharomyces cerevisiae to the multicellular green alga Volvox carteri (Fleischmann et al., 1995; Goffeau et al., 1996; Prochnik et al., 2010).

Highlights

I sometimes see them in my dreams
The colorful peaks and troughs, the sharp, crisp waves spread across my computer screen, the rolling nitrogenous mountains, each with its own nucleotide sitting solidly on the summit
Remember them? Those beautiful but oh so “oldgen” bioinformatics data generated from automated Sanger sequencing machines, such as the Applied Biosystems 370— the geriatric of genome sequencers

Summary

Introduction

I sometimes see them in my dreams. The colorful peaks and troughs, the sharp, crisp waves spread across my computer screen, the rolling nitrogenous mountains, each with its own nucleotide sitting solidly on the summit. The onslaught of next-generation sequencing (NGS) technologies (Metzker, 2010; Koboldt et al, 2013) and the access to previously unfathomable amounts of genomic data have made me dizzy, disillusioned, and anything but efficient. I’m constantly testing and learning the newest bioinformatics software and genome assembly programs.

Results

Conclusion