# SeroGen

> High-performance genomic analysis, de novo polysaccharide locus segmentation, and in silico serotyping

SeroGen: High-performance genomic analysis, single-pass bacterial & prophage ORF prediction, polysaccharide-specific 1D-CNN gene role classification, hybrid CNN-rescued MCL clustering, graph-based data structures, and de novo polysaccharide locus discovery.

## Overview & Architecture

- [Home](<https://seroverse.github.io/SeroGen/index.md>): Getting started, quickstart, and performance benchmarks
- [Architecture &amp; Algorithms](<https://seroverse.github.io/SeroGen/architecture/index.md>): Structure-of-Arrays (SoA) core, single-pass HMM-Viterbi ORF caller, polysaccharide-specific CNN role classifier, hybrid MCL clustering, graph data structures/GNN/arborescence, and de novo ACP-DP locus discovery

## Benchmarks &amp; Notebooks

- [Overview](<https://seroverse.github.io/SeroGen/notebooks/index.md>): Interactive Marimo benchmark notebooks and 16:9 slide decks
- [Prophage &amp; Bacterial ORFs](<https://seroverse.github.io/SeroGen/notebooks/prophage-orfs/index.md>): Single-pass bacterial and prophage ORF prediction benchmark on E. coli K-12 MG1655 (CP014225.1) and 9 embedded prophage islands
- [CNN Gene Role Classifier](<https://seroverse.github.io/SeroGen/notebooks/gene-classifier/index.md>): Polysaccharide-specific multi-scale 1D-CNN gene role classifier training, Optuna TPE tuning, and Numba layer representation sweep
- [S. pneumoniae De Novo CPS Database](<https://seroverse.github.io/SeroGen/notebooks/spneumo-serotyping/index.md>): S. pneumoniae de novo CPS locus discovery, hybrid MCL clustering, pan-locus graph construction, contig-split stitching, and database matching

## API Reference

- [serogen.core](<https://seroverse.github.io/SeroGen/reference/core/index.md>): serogen.core: SoA containers, sequences, alphabets, randstrobe indices, SW-Gotoh alignment, clustering, and graphs
- [serogen.genes](<https://seroverse.github.io/SeroGen/reference/genes/index.md>): serogen.genes: OrfPredictor, GeneRoleClassifier, GeneRoles, and Genes containers
- [serogen.loci](<https://seroverse.github.io/SeroGen/reference/loci/index.md>): serogen.loci: LocusSegmenter, LocusMatcher, LocusPredictor, and Locus/Loci models

## Community

- [Code of Conduct](<https://seroverse.github.io/SeroGen/conduct/index.md>): Contributor Covenant Code of Conduct
- [Contributing](<https://seroverse.github.io/SeroGen/contributing/index.md>): Local development setup, testing, and pull request guidelines
- [Release Notes](<https://seroverse.github.io/SeroGen/releases/index.md>): Version history and changelog