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Welcome to the stickleback genome browser.

  • This site contains the threespine stickleback genome assembly (v. 5) and the ninespine stickleback genome assembly (v. 7).

  • The browsers are built using the JBrowse2 platform, which allows for easy visualization of annotation tracks. For additional information about the JBrowse platform, including supported track formats, please see the documentation pages.

  • Additional genome linear views can be added to your working session by clicking "Add" in the menu bar, then "Linear Genome View."

  • Genomes can be compared by clicking "Add" in the menu bar, then "Linear Synteny View" or "Dotplot View." Alignments between genomes can be visualized by adding the optional existing synteny track.

  • Share your current working session with colleagues by clicking the share button on the top menu bar. This will generate a stable HTML link for your colleague to view the same region of the genome(s) as well as any feature tracks you have enabled.

Announcements

November 2022: The genome browser has been upgraded to JBrowse2.

December 1, 2020: liftOver chain files between the v. 5 genome and previous assemblies have been added to the data download page.

December 1, 2020: Full-length isoform sequencing was conducted on eight different tissues (Naftaly et al. 2020) and added as gene annotation tracks.

November 18, 2020: SNP variants from Puget Sound and Lake Washington (Shanfelter et al. 2019) have been integrated as browsable VCF annotation tracks.

July 6, 2020: The Stn microsatellite markers (Peichel et al. 2001) have been integrated as a searchable annotation track.

July 6, 2020: The v. 5 annotation files on the download page have been updated to a GFF3 file format.

July 6, 2020: The unplaced contigs in chromosome Un. have been updated in the browser and on the download page.

June 23, 2020: Annotations will be added regularly to the genome browser. Check back for updates.

June 23, 2020: LiftOver files are coming soon. Stay tuned to the download page.