Orphos CLI

Command-line interface for Orphos, a fast, parallel Rust implementation of Prodigal for finding protein-coding genes in microbial genomes.

Features

• 🚀 High Performance: Multi-threaded processing using Rayon
• 💾 Memory Efficient: Optimized for large genomes and metagenomic assemblies
• 🔄 Compatible: Output format compatible with original Prodigal
• 🌍 Cross-Platform: Works on Linux, macOS, and Windows
• 📊 Multiple Output Formats: GenBank, GFF3, SCO, and GCA formats
• 🧬 Flexible Modes: Single genome and metagenomic analysis modes

Installation

Using Cargo

cargo install orphos-cli

From Source

git clone https://github.com/FullHuman/orphos.git
cd orphos
cargo install --path orphos-cli

Homebrew (macOS/Linux)

brew tap FullHuman/orphos
brew install orphos

Conda

conda install -c bioconda orphos

Quick Start

Basic Usage

# Analyze a genome and output GenBank format
orphos -i genome.fasta -o genes.gbk

# Analyze with GFF3 output
orphos -i genome.fasta -f gff -o genes.gff

# Metagenomic mode for short contigs
orphos -i metagenome.fasta -p meta -o genes.gff

# Complete circular genome (closed ends)
orphos -i plasmid.fasta -c -o plasmid.gbk

Reading from stdin/stdout

# Input from stdin
cat genome.fasta | orphos -o genes.gbk

# Output to stdout
orphos -i genome.fasta > genes.gbk

# Pipe both
cat genome.fasta | orphos > genes.gbk

Command-Line Options

Required/Input

Output Options

Analysis Options

Other Options

Output Formats

GenBank (gbk)

Rich annotation format with gene features, translations, and metadata.

orphos -i genome.fasta -f gbk -o genes.gbk

GFF3 (gff)

General Feature Format version 3, widely used in genomics pipelines.

orphos -i genome.fasta -f gff -o genes.gff

Simple Coordinate Output (sco)

Tab-delimited gene coordinates for easy parsing.

orphos -i genome.fasta -f sco -o genes.sco

Gene Coordinate Annotation (gca)

Compact coordinate format.

orphos -i genome.fasta -f gca -o genes.gca

Analysis Modes

Single Genome Mode (default)

Use for complete or near-complete genomes (>100kb). Orphos will train on the genome to optimize gene prediction accuracy.

orphos -i complete_genome.fasta -o genes.gbk

Best for:

• Complete bacterial genomes
• Complete archaeal genomes
• Large contigs or chromosomes
• Closed genomes

Metagenomic Mode

Use for short contigs or mixed metagenomic assemblies. Uses pre-trained parameters instead of training on the input.

orphos -i metagenome_contigs.fasta -p meta -o genes.gff

Best for:

• Metagenomic assemblies
• Short contigs (<100kb)
• Mixed-species samples
• Fragmented sequences

Advanced Examples

Complete Circular Genome

For complete circular genomes (chromosomes, plasmids), use the -c flag to prevent genes from being called off the edges:

orphos -i circular_plasmid.fasta -c -o plasmid.gbk

Custom Translation Table

Specify a custom genetic code (translation table):

# Use translation table 4 (Mycoplasma/Spiroplasma)
orphos -i mycoplasma.fasta -g 4 -o genes.gbk

# Use translation table 11 (Bacterial and Archaea)
orphos -i bacteria.fasta -g 11 -o genes.gbk

Masking Low-Quality Regions

Mask runs of N's in low-quality sequences:

orphos -i draft_assembly.fasta -m -o genes.gff

Batch Processing

Process multiple genomes:

for genome in genomes/*.fasta; do
    base=$(basename "$genome" .fasta)
    orphos -i "$genome" -f gff -o "results/${base}.gff"
done

Pipeline Integration

Integrate with other bioinformatics tools:

# Find genes and extract protein sequences
orphos -i genome.fasta -f gff -o genes.gff
# ... then use genes.gff with other tools

# Combine with annotation pipelines
orphos -i assembly.fasta -p meta -f gff -o genes.gff
prokka --proteins genes.gff --outdir annotation genome.fasta

Performance Tips

1. Use multiple cores: Orphos automatically uses all available CPU cores via Rayon
2. Metagenomic mode for many small contigs: Faster than single mode for fragmented assemblies
3. Batch processing: Process multiple files in parallel using shell scripting
4. Large files: Orphos handles multi-GB files efficiently

Translation Tables

Orphos supports NCBI translation tables 1-25 (excluding 7, 8, 17-20). Common tables:

Related Projects

• orphos-core: Rust library for gene prediction
• orphos-python: Python bindings
• orphos-wasm: WebAssembly module for browser/Node.js

Contributing

We welcome contributions! Please see the main repository for contribution guidelines.

License

This project is licensed under the GPL-3.0 License - see the LICENSE file for details.

Citation

If you use Orphos in your research, please cite:

# TODO: Add citation information

Acknowledgments

This project is inspired by the original Prodigal by Doug Hyatt. We thank the authors for their groundbreaking work in prokaryotic gene prediction.

Support

• Issues: GitHub Issues
• Discussions: GitHub Discussions
• Documentation: docs.rs/orphos-cli