16sPIP is an integrative application that consists of a series of Perl, Python, and shell scripts that can be run in a Linux/Unix system. If you want to quickly detect pathogens in clinical samples based on 16S metagenomic sequencing, you could download and run this program directly. Or you could send us the raw data by email. Then we will do the analysis work for you. But this software and results could not be allowed to be used in any commercial work.


Download the latest version of the program here.


The most current Linux version of the manual is available here.


If you use the 16sPIP, please cite the following papers:
16sPIP: A Comprehensive Analysis Pipeline for Rapid Pathogen Detection in Clinical Samples Based on 16S Metagenomic Sequencing. BMC Bioinformatics, 2017


Q: Could I use this program under Windows system? 
A: No. This version of 16sPIP only works under Linux/Unix system.

Q: How many kinds of bacteria are currently covered by the database?
A: 252,567 reads were used as the 16S full-length bacterial reference database in 16sPIP, covering 15,217 species and 2,094 genera. 16S pathogen database was constructed from 29,258 total reads covering 346 bacterial species of human health concern in “The Directory of Pathogenic Microorganisms in Human Infections” published by the Ministry of Health of the People’s Republic of China.

Q: The pipeline provides two different working modes. How to choose an appropriate one when handing a sample?
A: Users could choose the fast mode of 16SPIP to quickly identify the existence of 346 pathogen bacterial species in their samples, which are directly related with human health. If users want to identity the existence of other species as well as to study the population diversity of microbiome, the sensitive mode is the better choice.

16sPIP Online Help

(File size can not exceed 100MB)

(File size can not exceed 100MB)

Powered by