HyperEx 🔬🧬

HyperEx (Hypervariable region Extractor) is a high-performance tool for precise extraction of 16S rRNA hypervariable regions using primer-based approaches. Built in Rust for speed and reliability.

Features ✨

• 🧬 Built-in universal 16S primer sequences
• 🔍 Supports IUPAC ambiguity codes in primers
• ⚡ Multi-threaded processing for large datasets
• 📁 Handles compressed inputs (gzip, xz, bzip2)
• 📊 Generates both FASTA and GFF3 outputs
• 🎯 Configurable mismatch tolerance

Installation 📦

Quick Install (via Cargo)

cargo install hyperex

Prebuilt Binaries

Download from our Releases Page

Download from Source

git clone https://github.com/Ebedthan/hyperex.git
cd hyperex
cargo install --path .

Usage 🚀

Basic Extraction

hyperex input.fasta

Extract Specific Regions

hyperex --region v3v4 --region v4v5 input.fasta

Custom Primers

hyperex -f CCTACGGGNGGCWGCAG -r GGACTACHVGGGTWTCTAAT input.fasta

With Mismatches

hyperex --region v1v2 --mismatch 2 input.fasta

Advanced Options ⚙️

Option	Description
-f, --forward-primer	Forward primer sequence (IUPAC supported)
-r, --reverse-primer	Reverse primer sequence (IUPAC supported)
--region	Predefined region (v1v2, v3v4, etc.) or primer file
-m, --mismatch	Allowed mismatches (default: 0)
-p, --prefix	Output file prefix (default: hyperex_out)
--force	Overwrite existing files
-q, --quiet	Reduce verbosity

Primer File Format 📝

Create a CSV file with primer pairs:

FORWARD_1,REVERSE_1
FORWARD_2,REVERSE_2
...

Examples 🧪

Multiple regions from compressed input:

xzcat big_file.fa.xz | hyperex --region v1v2 --region v3v4 -p results

Custom primers with 1 mismatch:

hyperex -f ATCG -r GGCC -m 1 input.fasta

Requirements ✅

• Rust 1.60+ (for source builds)
• Compression libraries (optional for compressed inputs):
• libz (gzip)
• liblzma (xz)
• libbz2 (bzip2)

Support 🆘

Found an issue? File it on our Issue Tracker.