Paired-ends data allows for much more powerful approaches to detecting genome rearrangements than single reads, and CLC Genomics Workbench therefore facilitates several ways of analyzing such paired end data.

Screenshot 1: Paired ends reads are shown with both sequences in the pair on the same line.

Much analysis can be carried out by working with the graphical options in CLC Genomics Workbench, and different colors are used for different types of data:

• The consensus and reference sequence is black per default.
• The forward reads (single reads) is green per default.
• The reverse reads (single reads) is red per default.
• The paired-ends reads is blue per default.
• Non-specific matches are yellow per default. This is when a read would have matched another place in the contig, it is considered a double match.

Screenshot 2: Coloring of the reads.

In addition to the user-defines coloring, CLC Genomics Workbench show three graphs of great value when inspecting the paired-ends reads:

• Paired-ends distance. Displays the average distance between the forward and the reverse read in a pair.
• Single paired-ends reads. Displays the percentage of the reads where only one of the reads in a pair matches the contig.
• Non-specific matches. Displays the percentage of the reads which match more than once.

Screenshot 3: More information about paired-ends reads can be displayed in the Side Panel.

These three graphs in combination with the read colors provide a great deal of information, guiding interpretations of the assembly result.