User interface

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MicrobeGPS user interface

MicrobeGPS will show the main window at startup. This window will display the data after analyzing the SAM files or loading previous analysis results. Below, you see a screenshot of the main window as it looks on a Windows 8 PC (it may look a little bit different on other systems). The four panels are explained in the following sections.

(1) Data panel

The data panel visualizes your analysis results. Basically, it lists all organisms found by MicrobeGPS, called Candidates. The list is ordered by the number of unique reads per candidate, starting with the most abundant one. Everything in the data panel is clickable. This means, if you double-click an item in the list, it will expand and show more detailed information. For example, if you expand a Candidate, it will show you all reference genomes supporting this particular candidate.

MicrobeGPS displays three categories of objects:

Candidates: A candidate represents what MicrobeGPS assumes a 'biological organism'. A candidate is described by one or more Supporting Genomes. These supporting genomes describe the taxonomic location of the organism; using the quality information (e.g. validity) you can estimate the distance between the true biological organism and the reference genome. This is what we call the [GPS principle] of MicrobeGPS. By double-clicking a candidate, you can view all its Supporting Genomes.

Supporting Genomes: Supporting genomes represent known organisms with available reference genomes (no matter if complete genomes or many contigs). This is where your reads were mapped to. When you expand a Supporting Genome, you have access to All Reads and the Unique Reads mapping to this genome and a list of Related Genomes that share reads with this genome, but support a different candidate. Note: Expanding All Reads or Unique Reads may take a while for large datasets.

Reads: A Read represents a single sequencing read from your dataset and has the same name as in the raw data. A shared read can be expanded to view all genomes to which the read was mapped, including the mapping error on the corresponding genome.

For each object, the table shows several columns with additional quantitative information about the object:

• [Reads]
• [Unique]
• [Coverage]
• [Validity]
• [Homogeneity]
• [Mapping Error]

(2) Visualization/Taxonomy tree panel

This panel is located in the upper right corner of the window. It has two tabs, one for graphics output and one showing a taxonomic tree. Further panels may be added by [Modules].

• Graphics panel: The graphics panel shows automatically generated info graphics. The type of the graphic strongly depends on which element you selected in the Data panel. When you click an item in the Data panel, MicrobeGPS generates a new graphic on the fly and discards the old one. The current graphic can be exported to file with the drop down menu Data -> Export Graphic. Below, you find a list of graphics MicrobeGPS generates.

  • Candidate: Pie chart showing the number of unique reads of each genome supporting this candidate.
  • Supp. Genome: The read mapping error histogram for the selected genome. Blue is the number of all reads, yellow is the number of unique reads.
  • 2 or 3 Supp. Genomes: Venn diagram showing the reads mapping to each genome as circle. Overlaps represent shared reads.

• Taxonomy tree panel: The taxonomy tree panel displays all genomes that were found by MicrobeGPS in a taxonomic tree. When a Supporting Genome or Candidate is selected in the Data panel, the taxonomy tree automatically highlights the selected elements in the tree and information about the number of mapped reads. Clicking on an element in the tree directly jumps to the corresponding candidate in the Data panel. Note that this information is only accessible if the reference genomes contained gi information.

(3) Settings/Modules panel

The Settings/Modules one settings tab and possibly some more module tabs. The settings tab provides some basic program settings, for example it allows you to switch off automated drawing of figures or updating the taxonomy tree. This is useful when you analyze large datasets and drawing the figures takes too long.

MicrobeGPS [Modules] often add their own tab to this panel. For example, the standard installation of MicrobeGPS includes a Search module, that allows you to search for reference genome names in the Data panel. Documentation about a module can be obtained in most cases by clicking on the tab; then the Help panel should show some information.

(4) Help/Console panel

The Help tab shows short descriptions and help texts. If you are not sure what a GUI element means or is used for, clicking on that element typically shows a brief description in this window.

The Console tab shows a list of messages generated by MicrobeGPS. If you encounter a problem, you will normally find error messages on this console.