Read2Ring 🧬🔁📊

A lightweight, cross-platform Bash pipeline that downloads SRA data, classifies with Kraken2, and visualizes taxonomic output with Krona.

Features

• FASTQ download & compression
• Kraken2 taxonomic classification
• Krona visualization (HTML donut)
• Easy installation (Conda or Docker)

Usage

bash Read2Ring.sh SRRNUM

# SRA → Kraken 2 → Krona

![CI](https://github.com/<USER>/SRA-Kraken-Krona/actions/workflows/ci.yml/badge.svg)
![License](https://img.shields.io/github/license/<USER>/SRA-Kraken-Krona)
![Issues](https://img.shields.io/github/issues/<USER>/SRA-Kraken-Krona)

A one-file Bash pipeline that downloads an SRA run, converts it to gzipped
FASTQ, classifies reads with Kraken 2, and produces an interactive Krona
donut—all in under 20 min on an M-series Mac or modern Linux laptop.

## Features

* Robust **prefetch** with HTTPS fallback
* Auto-detects CPU cores (`nproc` or `sysctl`)
* Works with **SRR / ERR / DRR** accessions
* Reproducible via Conda **or** Homebrew
* Single command to run, single HTML output

## Quick start (macOS)

```bash
brew tap brewsci/bio
brew install sratoolkit kraken2 krona pigz wget
# one-time Krona taxonomy build
/opt/homebrew/Cellar/krona/*/updateTaxonomy.sh ~/krona_taxonomy
chmod +x sra-to-krona.sh
./sra-to-krona.sh SRR33976478
open SRR33976478_run/SRR33976478_krona.html