Reefgenomics.Org - a repository for marine genomics data

Abstract

Over the last decade, technological advancements have substantially decreased the cost and time of obtaining large amounts of sequencing data. Paired with the exponentially increased computing power, individual labs are now able to sequence genomes or transcriptomes to investigate biological questions of interest. This has led to a significant increase in available sequence data. Although the bulk of data published in articles are stored in public sequence databases, very often, only raw sequencing data are available; miscellaneous data such as assembled transcriptomes, genome annotations etc. are not easily obtainable through the same means. Here, we introduce our website (http://reefgenomics.org) that aims to centralize genomic and transcriptomic data from marine organisms. Besides providing convenient means to download sequences, we provide (where applicable) a genome browser to explore available genomic features, and a BLAST interface to search through the hosted sequences. Through the interface, multiple datasets can be queried simultaneously, allowing for the retrieval of matching sequences from organisms of interest. The minimalistic, no-frills interface reduces visual clutter, making it convenient for end-users to search and explore processed sequence data. DATABASE URL: http://reefgenomics.org.

Figure 1.

Layout of http://reefgenomics.org. (A) Landing page shows the search bar and tiles corresponding to featured projects and a tile to explore all datasets. (B) Project page shows the typical layout of a project-specific page. Hovering the cursor over tiles darkens them, as shown in the ‘Browse’ tile.

Figure 2.

Visual exploration of genomic data accessible via the ‘Browse’ button. In this example, the repeats identified in the Aiptasia genome are overlaid on top of the gene models, allowing for a quick appraisal of genes with many repeat regions, and the relative position of these regions within the gene model.