3.9.4. Genome Assemblies¶
A genome assembly defines the chromosomes for a particular species and build. This definition includes the chromosome names and lengths, as well as the order in which they are arranged when displayed in a genome browser. GenomeBrowse use the current genome assembly so that plotted features will be arranged according to its chromosome definition. The species and build specified by the selected genome assembly is used to manage annotation and data sources within GenomeBrowse. This functionality is intended to help prevent accidental alignment of annotation data to the wrong genome assembly.
A genome assembly can be selected from the list of bundled genome assemblies, downloaded from the genome assemblies data repository from Golden Helix, created from a marker mapped spreadsheet, or created from a marker map. This enables the user to create a genome specific to the data at hand or for a species not in the list of bundled species.
The current genome assembly can be selected through the tool bar controls of GenomeBrowse. The genomes available can be viewed through the project navigator menu item, Tools > Manage Genome Assemblies.
Bundled Genome Assemblies¶
Basic genome assemblies for several species are made available with GenomeBrowse. The initial list of chromosome definitions to provide was based on those available within the Integrated Genome Browser (IGB) http://www.bioviz.org. Additional species and builds have been added to the bundled genome assemblies since then.
If genome information for a particular species and build is available and is not yet included in the bundled builds, you can convert that information into a genome assembly at the same time as converting a Reference Sequence to a TSF annotation source. See Convert a 2Bit File or Converting a FASTA File.
Switching Genome Assemblies¶
The genome assembly can be changed by choosing a new genome assembly in the GenomeBrowse tool bar controls.
Using Tool Bar Controls to Switch Genomes¶
GenomeBrowse has genome assembly information located on the tool bar. The control menu contains a list of all system and user genome assemblies. Recently used genome assemblies are listed at the top, all genomes are listed in alphabetical order under the black bar.
To change the genome to a different species or build, select the desired genome assembly from the list.
After changing the current genome assembly, the user will be asked if the reference sequence track should be downloaded if it is not found in the local annotation folder. Selecting Yes will start the download of the annotation track. Analysis and visualization of the data can continue while the file is being downloaded except for BAM files. Selecting No will not download the reference file so that coverage for BAM files will not be able to be computed.
Switching the genome assembly will cause the data to be re-plotted with the new mapping and the zoom to be reset showing all of the data.
If annotation tracks that do not correspond to the current species and build features are plotted the data may not be correctly aligned to the genome.
Managing Genome Assembly Views¶
Located in the GenomeBrowse tool bar to the right of the genome assembly control menu is the Hide/Show eyeball icon, clicking this icon allows the user to manage the existing segments present in the selected assembly.
The Genome Segment Order and Visibility dialog will contain a list of each unique segment identified in the data loaded into the GenomeBrowse window. Segments can represent chromosomes, scaffolds, contigs or a combination of all three.
The user can hide or show segments by checking or unchecking the box in the Visible column. A checked box will say Yes indicating the data from that segment will remain visible in your GenomeBrowse plot and an unchecked box will say No indicating that segment and all data in that segment will be hidden.
Segment order can also be rearranged by highlighting a segment and using the up/down arrows to the right of the segment list, the single arrows will move the segment one position at a time and the double arrows will move the segment all the way to the top or bottom of the list. Additionally the user may specify the amount of visible space they would like between the segments by entering the base pair distance in the Space box.
At any point the user may restore the original order and visibility of the segments based on the genome assembly file by clicking Restore Defaults. Once changes are complete click OK to implement then in the GenomeBrowse window.