Usage patterns Running JBrowse with the pre-indexing scripts If JBrowse is to be used as a broad-access viewing portal to a genome annotation database, the greatest efficiency can be gained by using the pre-indexing scripts in the top-level bin/directory. These include prepare-refseqs (for indexing a FASTA file containing the reference sequences and breaking the sequences into manageably-sized chunks), flatfile-to-json (for importing a GFF, BED, or GenBank file as a track), add-bw-track (for importing a BigWig file as a track), and various other utility scripts for adding and removing track configuration stanzas and otherwise managing the track list. Alternatively, the tracks can be loaded directly from a Bioperl-compatible database such as Chado [35] using the biodb-to-json loader script. The final step in this workflow is to build the index of feature and region names using the generate-names script. Running JBrowse without the pre-indexing scripts When standard-format data files are available on the local filesystem (or at a remote URL), a FASTA file can be loaded directly via the Genome menu and annotation tracks can then be created by loading BAM, Wiggle/BigWig, GFF, or VCF files directly via the Track menu. These formats can now be directly consumed by JBrowse (from files or URLs) without the need for JSON indexing; BAM files must, however, be indexed with a BAM index (.bai) file and VCF files with a tabix index (.tbi) file, which may be generated using utilities such as SAMTools [40]. JBrowse uses these index files and HTTP range-request headers to retrieve only the content that it needs to render the particular region in view, allowing very large data files (such as BigWig, BAM, VCF + Tabix, GFF3 + Tabix, or FASTA + faidx) to be browsed quickly over the network in an efficient random-access way. Running JBrowse as part of a larger web application JBrowse can be embedded in a larger web application with its own data sources. The encompassing framework can use the indexing scripts to load data or to directly generate the JSON index files which JBrowse consumes; alternatively, data sources can be provided as a web service (there is a REST API for most features). JBrowse can be started in “embedded mode” (with many user interface features disabled) for compactness. Numerous callbacks are available to implement context-specific actions when the user interacts with the sequence and annotations. Embedding a genome browser in a web application framework has many advantages over a desktop system; for example, users can, in principle, share data and views instantly over the web rather than resorting to sharing screenshots via a side-channel (email). Running JBrowse on the UCSC genome database The ucsc-to-json script can be used to import a UCSC genome database, creating JBrowse index files directly from a UCSC database dump. Demonstration instances for the latest JBrowse release on several genome data sets can be found at http://jbrowse.org/demos. Running JBrowse as a desktop application JBrowse can also be run as a cross-platform desktop application, entirely independently of a web browser, using the Atom Electron framework (atom). The data can be connected to desktop JBrowse in at least two ways: the index files that are generated by the indexing scripts (and normally hosted on the server) can be bundled with the JBrowse application or JBrowse can be used to browse local data files.