EnteroBase SNPs JBrowse¶
In an EnteroBase SNP project (see SNP Projects), it is possible to visualize the SNPs with respect to the reference using a window which is an instance of JBrowse. JBrowse provides genome browser functionality which is described on this page. This allows scrolling and zooming through the genome with a track selector controlling what data is displayed.
The JBrowse window has its own online
documentation accessible from the Help menu at
Help -> ? General which
covers all of the basics of using the JBrowse graphical user interface. The documentation below
repeats some information available from the online help and also includes
some EnteroBase specific information.
The view can be moved/ scrolled by clicking and dragging in the track area or by clicking the left and right arrows in the navigation bar or by pressing the left and right arrow keys while holding down “shift”.
Zooming in and out¶
When the JBrowse window is first opened, the default tracks selected are “Prokka Annotation”, “wgMLST” and “Reference sequence”. (It is likely that the initial zoom level will not allow reading the bases in the reference sequence. Zooming in may be necessary in order to make the bases readable and also to read the annotations from Prokka or wgMLST - or other - loci.)
Zooming in can be achieved by clicking the magnification glass icon with a plus sign in the navigation bar, pressing the up arrow key while holding down the shift key and also by double-clicking in the main display area.
Similarly, zooming out is done by clicking the magnification glass icon with a minus sign in the navigation bar, pressing the down arrow key while holding down the shift key and double-clicking in the main display area with the shift key held down.
It is also possible to zoom into a specific area of the display area by using “rubber-band” zooming (or “dynamic zooming”). In order to “rubber-band” zoom, click on one end of the targeted area with the shift key held down. Then, continuing to hold down the mouse button, drag the mouse to the other end of the target area. The targeted area will expand to fill the main display area.
The available tracks in EnteroBase are organised in three main areas in the track selector which is on the left hand side of the display. The top area of the track selector include tracks for the EnteroBase genotyping schemes (such as Achtman 7 Gene and cgMLST), Prokka annotation, repeat/ masked regions and assembly errors. The tracks in the top area of the track selector are not specific to the datasets/ strains included in the SNP project. The middle area of the track selector is for the reference sequence track. The bottom area of the track selector - with the heading “snp” - is for tracks with the SNPs in all of the strains in the SNP project.
The tracks currently displayed may be changed by clicking on the tick/ check box next to the track’s name in the track selector on the left hand side of the display. (This track selector differs from the “track list” and also the more complex “faceted track selector” referred to in some of the JBrowse documentation.) A track may also be unselected by clicking on the circled cross icon on the left end of the track label for the track in the main display area. (Other options for manipulating the track are available by clicking on the downward arrow which appears on mousing over the track label.)
The tracks in the main display area may be put into any desired order by dragging and dropping the track labels on the left hand side (in the main display area, not the track selector).
It is possible to search for either a feature or reference sequence by typing its name into the location box in the JBrowse window and pressing Enter. Then the display will jump to that feature or reference feature. Also, while typing in a feature name, JBrowse will provide suggestions. A particular suggestion may be chosen by clicking on the suggestion in the dropdown menu that appears and clicking on the “Go” button.
Example searches are described for the “workshop_snp” project in the Escherichia database. Trying these searches will require going to the Escherichia database page and clicking on “Load Workspace” on the right hand side of the page near the top. Then click on “workshop_snp” and press the “Load” button.
lacZ will jump to the feature with that name. (Also, notice that typing “lac” alone will provide a number of
25000 will centre the display at base 25000 on the current sequence (for the current contig).
NODE_5_length_173547_cov_28.7718_ID_9 jumps to contig with name NODE_5_length_173547_cov_28.7718_ID_9
NODE_6_length_151020_cov_31.5251_ID_11 jumps to contig with name NODE_6_length_151020_cov_31.5251_ID_11
NODE_2_length_244251_cov_28.0988_ID_3:670..2417 jumps to the region on the contig NODE_2_length_244251_cov_28.0988_ID_3 between 670 and 2417