Contig Assembly window

The assembly window consists from 3 parts:

- the CONTIG MAP
- the CONTIG GRID (the middle part of the picture below), this is were the assembled sequences and the consensus contig are displayed
- the CHROMATOGRAM VIEWER, 'were the corresponding chromatograms are displayed

The CONTING MAP, the CONTIG GRID and the CHROMATOGRAM VIEWER are correlated, resulting in a synchronized display of the chromatograms, contig and contig map. This makes the correction of ambiguous bases much faster and easier.

  - use this button to navigate from ambiguous base to ambiguous base.

- use this button to navigate from ambiguous base to ambiguous base.

- use this button to save changes to the contig

- use this button to see the contig how it is saved on disk

 - use this to scroll the selected chromatogram

- use this trackbar (in the selected chromatograms) to move the position of the bases relative to the peaks

- show / hide the trackbar for the peak height

- show / hide the contig map

- use this trackbar to increase/decrease peak height in the selected chromatogram

Colors in DNA Baser

In the CONTIG GRID, the ambiguous bases are highlighted with the red color.
The bases removed following end trimming have a gray background. The recognition sequences used for vector removal are highlighted in light blue:

Automatic trimming engine

DNA Baser is removing automatically the low quality ends from the chromatograms before starting the assembly process. Please see details about this important process here.