JBrowse is a fast and full-featured genome browser built with JavaScript and HTML5. It is easily embedded into websites or apps but can also be served as a standalone web page. Overall improvements to speed and scalability are accompanied by specific enhancements that support complex interactive queries on large track sets. Analysis functions can readily be added using the plugin framework; most visual aspects of tracks can also be customized, along with clicks, mouseovers, menus, and popup boxes. JBrowse can also be used to browse local annotation files offline and to generate high-resolution figures for publication. JBrowse is a mature web application suitable for genome visualization and analysis.

Genome annotation is the process of identifying the location and function of a genome’s encoded features. Improving the biological accuracy of annotation is a complex and iterative process requiring researchers to review and incorporate multiple sources of information such as transcriptome alignments, predictive models based on sequence profiles, and comparisons to features found in related organisms. Because rapidly decreasing costs are enabling an ever-growing number of scientists to incorporate sequencing as a routine laboratory technique, there is widespread demand for tools that can assist in the deliberative analytical review of genomic information. To this end, Apollo is an open source software package that enables researchers to efficiently inspect and refine the precise structure and role of genomic features in a graphical browser-based platform. In this paper we first outline some of Apollo’s newer user interface features, which were driven by the needs of this expanding genomics community. These include support for real-time collaboration, allowing distributed users to simultaneously edit the same encoded features while also instantly seeing the updates made by other researchers on the same region in a manner similar to Google Docs. Its technical architecture enables Apollo to be integrated into multiple existing genomic analysis pipelines and heterogeneous laboratory workflow platforms. Finally, we consider the implications that Apollo and related applications may have on how the results of genome research are published and made accessible. Source: https://github.com/GMOD/Apollo License (BSD-3): https://github.com/GMOD/Apollo/blob/master/LICENSE.md Docker: https://hub.docker.com/r/gmod/apollo/tags/ , https://github.com/GMOD/docker-apollo Requirements: JDK 1.8, Node v6.0+ User guide: http://genomearchitect.org ; technical guide: http://genomearchitect.readthedocs.io/en/latest/ Mailing list: apollo@lists.lbl.gov

GrainGenes is the USDA-ARS database and Web resource for wheat, barley, oat, rye, and their relatives. As a community Web hub and database for small grains, GrainGenes strives to provide resources for researchers, students, and plant breeders to improve traits such as quality, yield, and disease resistance. Quantitative trait loci (QTL), genes, and genetic maps for quality attributes in GrainGenes represent the historical approach to mapping genes for groat percentage, test weight, protein, fat, and β-glucan content in oat (Avena spp.). Genetic maps are viewable in CMap, the comparative mapping tool that enables researchers to take advantage of highly populated consensus maps to increase the marker density around their genes-of-interest. GrainGenes hosts over 50 genome browsers and is launching an effort for community curation, including the manually curated tracks with beta-glucan QTL and significant markers found via GWAS and cloned cellulose synthase-like AsClF6 alleles.