Genome information#
Genome assembly score#
Genome assemblies are ranked by a quality score.
These scores are solely meant to rank the assemblies and be able to show and recommend a best available assembly per strain.
Genome assembly scores
Assembly score calculation#
| Condition | Score adjustment |
|---|---|
| Start value | score = 100 |
| Not included in RefSeq | score – 25 |
| GenBank status “suppressed” | score - 50 |
| GenBank status “replaced” | score - 30 |
| Number of contigs | score – (number of contigs / 5) |
| CheckM completeness | score – (100 – completeness) |
| CheckM contamination | score – contamination |
Negative scores are set to zero.
Genome browser#
For each strain, the best genome assembly that is available in the INSDC databases (GenBank, ENA, DDBJ) is displayed in a genome browser. The annotations shown in the genome browser were created using the Bakta tool.
The genome browser
All contigs of the assembly are listed as buttons in a box in the upper left corner of the genome browser . The button for the contig currently displayed in the viewer is highlighted in dark gray. Clicking on a different contig button changes the display.
An annotation summary box can be found in the upper right corner .
The viewer consists of two panels. The upper panel shows annotations on the forward (top) and reverse strands (bottom) over the complete selected contig . The area highlighted by the red sliding window is shown in greater detail in the bottom panel of the viewer . The selected area can be manipulated by sliding the red highlighter or by typing coordinates into the 'Start' and 'End' input fields above the viewer .
Users can explore features annotated on the genome further by clicking the 'Show feature table' button . This opens a searchable and filterable list of all annotations.
The feature table with active filters
The feature table can be filtered by feature type and contig and be searched by text . Active filters are shown above the table and can be deactivated by clicking the red active filter buttons .
Clicking on a feature in the bottom panel of the viewer or in the feature table opens a detail view displaying the gene sequence of the feature.
The gene sequence detail view