Modules

The CAP divides modules into five subpipelines covering: quality control, preprocessing to remove low quality and contaminat sequences, analysis of short reads, analysis of assemblies, and constructing relevant databases and indices for the other four pipelines. Detailed descriptions for each subpipeline and the modules within may be found below.

Each link contains a description of the subpipeline, and a list of modules in the pipelines with descriptions and links to example outputs from each module.

Documentation:

• Quality Control
• Preprocessing
• Short Read
• Assembly
• Databases