Question:

What steps are involved in utilizing ABySS-Explorer to examine the connections between contigs?

Answer:

ABySS-Explorer is a powerful tool designed to visualize genome sequence assemblies and analyze contig connectivity. Here’s a step-by-step guide on how to use ABySS-Explorer for this purpose:

: Before starting, make sure your system meets the requirements, including Java SE Runtime Environment 6 or above.

2.

Prepare Assembly Files

: Your assembly must be generated by ABySS 1.2.0 or above, with all related files placed in the same directory.

3.

Launch ABySS-Explorer

: Use the command `java -jar [argument]` to launch the application, where `` is the path to the ABySS-Explorer JAR file.

4.

Import Assemblies

: Once the application is running, import your assemblies using the provided buttons. The assemblies panel will help you manage and select the assemblies you wish to view.

5.

Navigate the Interface

: Familiarize yourself with the user interface, which includes the Assemblies Panel, Settings Panel, Statistics View, Plots View, Navigator View, and Search Box.

6.

Examine Contig Connectivity

: In the Navigator View, you can explore the graph-based representation of the sequence assembly. This view is particularly useful for examining contig connectivity and supporting paired-end read relationships.

7.

Utilize Miscellaneous Features

: ABySS-Explorer also offers various features like BLAT search, which can be accessed if an internet connection is available.

By following these steps, you can effectively utilize ABySS-Explorer to analyze the connections between contigs, gaining insights into the structure of genome assemblies.