NGPINT V3: a containerized orchestration Python software for discovery of next-generation protein–protein interactions

TL;DR

NGPINT V3 is an updated software for analyzing protein–protein interactions using containerization to improve compatibility and ease of use.

Contribution

NGPINT V3 introduces containerized deployment with Singularity and Docker for cross-platform accessibility and streamlined workflows.

Findings

Container images are hosted on Sylabs and Dockerhub for easy integration into high-throughput and cloud workflows.

The software is now more compatible and easier to install, resolving previous dependency issues.

Full documentation and software are available on GitHub and Zenodo.

Abstract

Batch yeast two-hybrid (Y2H) assays, leveraged with next-generation sequencing, have afforded successful innovations for the analysis of protein–protein interactions. NGPINT is a Conda-based software designed to process the millions of raw sequencing reads resulting from Y2H–next-generation interaction screens. Over time, increasing compatibility and dependency issues have prevented clean NGPINT installation and operation. A system-wide update was essential to continue effective use with its companion software, Y2H-SCORES. We present NGPINT V3, a containerized implementation built with both Singularity and Docker, allowing accessibility across virtually any operating system and computing environment.

This update includes streamlined dependencies and container images hosted on Sylabs (https://cloud.sylabs.io/library/schuyler/ngpint/ngpint) and Dockerhub (https://hub.docker.com/r/schuylerds/ngpint), facilitating easier adoption and integration into high-throughput and cloud-computing workflows. Full instructions and software can be also found in the GitHub repository https://github.com/Wiselab2/NGPINT_V3 and Zenodo https://doi.org/10.5281/zenodo.15256036.

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