PANGEA: pipeline for analysis of next generation amplicons

PANGEA offers a streamlined, efficient pipeline for analyzing high-throughput DNA sequencing data, enabling rapid identification and comparison of microbial communities. This Perl-based tool processes sequences from next-generation sequencers into formats compatible with BLAST and other databases, facilitating quick assessments on personal computers. Demonstrated using 16S rRNA sequences from Hawaii Volcanoes National Park soils and rat stool samples, PANGEA simplifies complex bioinformatics workflows—from pre-processing to classification—across Mac OSX, Windows, or Linux platforms. Its modular design allows users to customize databases or run the entire pipeline as a single script, 'backbone,' excluding only the chi² step. This innovation accelerates environmental and clinical microbial studies by reducing computational barriers.

Giongo, A., Crabb, D. B., Davis-Richardson, A. G., Chauliac, D., Mobberley, J. M., Gano, K. A., Mukherjee, N., Casella, G., Roesch, L. F. W., Walts, B., Riva, A., King, G., & Triplett, E. W. (2010). PANGEA: pipeline for analysis of next generation amplicons. The ISME Journal, 4(7), 852–861. https://doi.org/10.1038/ismej.2010.16