Welcome to PuMA’s documentation!

PuMA’s code can be found here. PuMA is also available through iMicrobe.

About PuMA

PuMA is a pipeline written in Python3 for papillomavirus genome annotation.

The pipeline was created by utilizing several Python3 and command line packages including Biopython, BLAST, MEME, FIMO, and MUSCLE as well as user defined functions. For more information on how PuMA works, refer to ‘How PuMA Works’.

Contents:

• Dependency Information
• Local Usage (MacOS or Linux)
• Usage via Docker
• Usage via iMicrobe
• Input File formatting
• Output
• How PuMA Works
• License

Support

For questions, contact Dr. Koenraad Van Doorslaer via vandoorslaer AT arizona DOT edu or visit the KVD Lab website.