These scripts are DEPRECATED and are unlikely to be work or be useful. See the metabarcoding and barcoding pipelines in my pipelines repository, or learn more about metabarcoding at our Learn Metabarcoding course.
NAPtime is a set of perl scripts to efficiently process amplicons from NGS.
You can find the documentation for the scripts at https://github.com/tjcreedy/NAPtime/wiki
They are designed for use by the Vogler Lab at the Natural History Museum, London, UK, but anyone is free to use the scripts according to the terms of the license. As detailed in the wiki, the scripts call many external programs, which are assumed to be installed and on the PATH of the current user. The scripts do not currently check that the external programs are installed, and will fail in all sorts of weird and wonderful ways.
The scripts were written by Thomas J. Creedy as part of his PhD in the Vogler Lab. They are maintained and updated as need and time allows. The scripts are provided with no warranty, and absolutely no guarantee that they won't do something slightly wrong that renders your data meaningless.
If you want help using the scripts after reading the wiki, you are welcome to get in touch and I'll attempt to provide basic support as my time allows. If you want new features (e.g. new external program calls) added, I'm very open to ideas. If you find a bug, please let me know!