• be in fasta format.

• contain multiple sequences.
• contain both lower and upper case characters.

• contain nucleic acid notation that deviates from the basic (ACGT) notation as this can creates artifactual outlier.
• contain multiple sequences with the same name descriptor.
• contain DNA sequences shorter than the given fragment length.

1. contig position data - PC1 x PC2 Position data that denotes the projections of each fragment onto the first and second eigenvector. Format is: "sequence name","fragment position","PC1","PC2" Here each line in the csv-file denotes one DNA sequence fragment vector that has been generated and projected onto the first respectively second eigenvector of the whole data set.
2. contig position data - PC2 x PC3 Position data that denotes the projections of each fragment onto the second and third eigenvector. Format is: "sequence name","fragment position","PC2","PC3" Here each line in the csv-file denotes one DNA sequence fragment vector that has been generated and projected onto the second respectively third eigenvector of the whole data set.
3. contig position data - PC1 x PC3 Position data that denotes the projections of each fragment onto the first and third eigenvector. Format is: "sequence name","fragment position","PC1","PC3" Here each line in the csv-file denotes one DNA sequence fragment vector that has been generated and projected onto the first respectively third eigenvector of the whole data set.
4. cumulative eigenvalue plot csv-file that contains the cumulative eigenvalue of the whole data set. It indicates how much of the data set variance is described by the plotting the data sets in regard to the first three eigenvectors.

Viewer

The overview shows all three pca-plots and the eigenvalue plot. The axes are labled with the corresponding principal component and the amount of variance it is representing. By clicking one specific plot, a more detailed view is shown.

After loading, the first ten contigs will be selected. Additional contigs can be highlighted by either selecting the line in the graph directly or using the corresponding legend item. Analog, contigs can be deselected and they will fade into the background.

• Overview Switchs back to the overview page.
• toogle Hides current selection in the graph for better overview. The selected contigs will stay visible in the legend. dditional contigs can be selected, another toggle merges the old selection with the new selected contigs.
• select all Select all contigs.
• deselect all deselect all contigs
• reset Highlights the first ten contigs, therefore the inital selection is restored.

All selections will simultaneously be visible in the other smaller plots. Selecting one of these will change the detailed view. Also the eigenvalue plot can be selected this way.

The detailed view of the partial sums of eigenvalues allows to evaluate the variance of the underlying data.