Fig. 1

The dramatic increase in the rate and amount of sequencing. a Next generation sequencing (NGS) reads have become the dominant form of sequence data. This is illustrated in a graph of National Institutes of Health (NIH) funding related to the keywords “microarray” and “genome sequencing”, which shows increasing funding for NGS and decreases in the funding of earlier technologies such as microarrays. b The size and growth rate of the Sequence Read Archive (SRA) highlight the importance of efficiently storing sequence data so that they can be accessed by the broader scientific community. The SRA’s centrality in the storage of DNA sequences from next-generation platforms means that it also serves as a valuable indicator of the scientific uses of sequencing. Furthermore, the rise in protected sequence data highlights the challenges facing genomics as ever-greater amounts of personally identifiable sequence data are being generated. c It is interesting to look at the contribution of large sequence depositions compared to smaller submissions. This provides an indication of the size distribution of sequencing projects. At one end of this size spectrum are large datasets generated by the collaborative effort of many labs. These include projects that have taken advantage of sequencing trends to generate population-scale genomic data (1000 Genomes) or extensive characterization of cancer genomes by The Cancer Genome Atlas (TCGA). On top of generating a vast amount of sequencing data with the aim of better understanding human variation and disease, high-throughput sequencing has dramatically expanded the number of species whose genomes are documented. The number of newly sequenced genomes has exhibited an exponential increase in recent years. Entries with asterisks indicate projects that produce open access data. ADSP, Alzheimer’s Disease Sequencing Project; HMP, Human Microbiome Project. d A more detailed analysis of the SRA illustrates the pace at which different disciplines adopted sequencing. Plots depicting the cumulative number of bases deposited in the SRA and linked to papers appearing in different journals provide a proxy for sequencing adoption. More general journals such as Nature and Science show early adoption. Meanwhile, SRA data deposited by articles from more specific journals such as Nature Chemical Biology and Molecular Ecology remained low for a relatively long period before increasing. These trends highlight the spread of sequencing to new disciplines. e Sequence data have also been distributed over the tree of life. In terms of size, the vast majority of sequence data generated have been for eukaryotes. This is due in part to the larger genome size of eukaryotes and to efforts to sequence multiple individuals within a given species, especially humans. In terms of the number of species sequenced, prokaryotes are by far the best represented. Moving forward, the continuing decrease in the cost of sequencing will enable further exploration of genetic diversity both within and across species. Data were obtained from GenBank