Collect Paired Read Statistics

The Collect Paired Read Statistics tool identifies paired reads between pairs of contigs and can be used to collect evidence for how contigs are positioned to one another. Hence, the Collect Paired Read Statistics tool provides information about potential overlaps and unknown gaps between pairs of contigs, which further can be visualized when combined with the Align Contigs tool. The tool searches for broken paired reads in all contig read mappings and for each broken paired read that is identified, the contig with the mate read is registered. The output is a table summarizing occurrences of these events, name of the involved contigs as well as the orientation and distance between the contigs relative to each other.
Paired reads with one read in one contig and the mate read in another contig are often reported in cases with many sequencing errors or areas with repeats. In these cases, the de Bruijn graph has not been capable of using the paired reads in the assambly process, which instead are reported in the Paired Read Statistics table.