This is a nice tool, but very difficult to use. It could be improved greatly which could make it into really great software but there is nobody around to deal with real user issues... as seen by the lack of response in the online discussion forum. 1. If files are not in the expected format [eg. Fasta read names have to conform to an unadvertised standard], you do not get any warning or explanation why it failed. 2. If a stage fails, you do not get any notification. You have to search inside another file to find out whether it even worked. It should at least tell you "Errors happened. Look at <filename.err> for more details" or "No errors detected." 3. There is no easy way to take the best advantage of multiple cores. You can set an option within the Protocols XML file. And in some cases you can set an option via "-x" in the command line. But if I examine the load and CPU utilization of all cores, I can see that it rarely uses more than one core at the same time and in some stages, it never uses the number of cores specified. 4. Most of the user configurable options have unclear meaning. You have to read into the program code to figure out how they are really used. 5. Hardly any response to user input. There is a discussion forum but virtually no activity or response from anyone involved with the software. It appears to be abandon-ware.