PUPpy: a primer design pipeline for substrain-level microbial detection and absolute quantification.

ABSTRACT: Characterizing microbial communities at high resolution and with absolute quantification is crucial to unravel the complexity and diversity of microbial ecosystems. This can be achieved with PCR assays, which enable highly selective detection and absolute quantification of microbial DNA. However, a major challenge that has hindered PCR applications in microbiome research is the design of highly specific primer sets that exclusively amplify intended targets. Here, we introduce Phylogenetically Unique Primers in python (PUPpy), a fully automated pipeline to design microbe- and group-specific primers within a given microbial community. PUPpy can be executed from a user-friendly graphical user interface, or two simple terminal commands, and it only requires coding sequence files of the communi

SUBMITTER: Ghezzi H 

PROVIDER: S-EPMC11288016 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature