cloneArmy 0.1.1

Analyze haplotypes from Illumina paired-end amplicon sequencing

CloneArmy

CloneArmy is a modern Python package for analyzing haplotypes from Illumina paired-end amplicon sequencing data. It provides a streamlined workflow for processing FASTQ files, aligning reads, and identifying sequence variants.

Features

• Fast paired-end read processing using BWA-MEM
• Quality-based filtering of bases and alignments
• Haplotype identification and frequency analysis
• Rich command-line interface with progress tracking
• Comprehensive output reports
• Multi-threading support

Installation

pip install cloneArmy

Requirements

• Python ≥ 3.8
• BWA (must be installed and available in PATH)
• Samtools (must be installed and available in PATH)

Usage

Command Line Interface

# Basic usage
cloneArmy /path/to/fastq/directory reference.fasta

# With all options
cloneArmy /path/to/fastq/directory reference.fasta \
    --threads 8 \
    --output results \
    --min-base-quality 20 \
    --min-mapping-quality 30

Python API

from pathlib import Path
from clone_army.processor import AmpliconProcessor

# Initialize processor
processor = AmpliconProcessor(
    reference_path="reference.fasta",
    min_base_quality=20,
    min_mapping_quality=30
)

# Process a single sample
results = processor.process_sample(
    fastq_r1="sample_R1.fastq.gz",
    fastq_r2="sample_R2.fastq.gz",
    output_dir="results",
    threads=4
)

# Results are returned as a pandas DataFrame
print(results)

Output

For each sample, CloneArmy generates:

• A sorted BAM file with alignments
• A CSV file containing haplotype information:
  • Sequence
  • Read count
  • Frequency
  • Number of mutations
• Console output