The contig analysis table

The contig analysis generates a table that lists start and end position as well as length of all problematic regions detected for each contig. The table provides an overview that allows for manually discriminating actual misassemblies from correct assemblies. The table by itself does not give access to editing the data: this needs to be done either directly in the contig sequence (possibly with reads mapped) or through the contig aligner.

A good starting point for the further analysis can be to look in the top left corner of the table where the number of rows in the table is shown. In cases with many rows it can be an idea to adjust some of the parameters in order to potentially remove false positive results and thereby reduce the number of rows. When the parameter settings have been optimized, the table can be used for manual evaluation of the problematic regions by using the filter tool for example.