cWGAP run best when using finished sequence - it becomes less reliable with draft sequences, or poorly assembled genomes. Following the rule: Garbage in garbage out. Think about that in life too.
Wait.. what is finished? “Finished sequence” refers to a region of DNA which has been closed to a point where there are no gaps or only well-characterized ones that cannot be resolved for biological reasons. According to the human genome project, “finished sequence” must also be 99.99% accurate, containing error rates of less than 1 error in 10,000 assembled bases. This momentous endeavor created a gold-standard for accuracy of finished genomes. Subsequent projects that have similar high levels of support have also finished genomes to high standards, but many recently completed NGS genome projects, lacking the same financial resources, have generated low-quality drafts containing unresolved ‘resolvable’ gaps. Generating accurate genome sequences and genome annotation are important but time-consuming aspects of de novo genome sequencing projects. Since it was considered desirable for the APEC toolbox to contain high quality, finished genomic sequences, a significant amount of time and resources were expended to generate the best-finished quality sequences possible and make them available for future analysis.