DEEPN v7 and Stat Maker v7 and new MAPster released: tools for yeast two-hybrid NGS analysis and fastq mapping

DEEPN (Dynamic Enrichment for Evaluation of Protein Networks) is our lab's fully integrated suite of processing and analysis programs for batch yeast two-hybrid (Y2H) screens: from fastq to prey fragment discovery. It maps raw sequencing reads (MAPster), counts them per candidate gene, extracts junction sequences, and statistically ranks candidate protein-protein interactions. Stat Maker is the statistics module at its core.

Version 7 adds a more rigorous statistics panel for calling hits: a dual-model agreement gate (DESeq2 fold-change plus a Bayesian-adjusted enrichment estimate must each independently clear threshold before a gene is called), two complementary p-value calculations users can choose between depending on how strongly a given screen's baits deplete their control population, and a results table built for scanning large candidate lists quickly.

DEEPN's FragFinder tool pulls the exact sequencing reads and junction calls that a hit has so that fragments can be predicted, synthesized and re-tested.

This release also brings updates to MAPster, the companion tool that maps raw sequencing reads onto the reference genome ahead of a DEEPN analysis: a native Apple Silicon build for faster mapping on newer Macs, an option to export alignments as compact .bam files alongside the existing .sam output, and a streamlined mode that launches MAPster directly from DEEPN so the whole pipeline lives in one place. MAPster runs on the HiSAT2 engine.

DEEPN and Stat Maker (including a standalone Stat Maker build for labs that just need the statistics module) are free, open-source, and available as native Apple Silicon Mac apps from our GitHub page:

https://github.com/RobertPiper/DEEPN/releases