KIRAL

KIRAL is a fast and efficient tool for aligning sequencing reads to a database of over 1600 Killer Immunoglobulin-like Receptor (KIR) allele sequences. Designed for genomic research and immunological studies, KIRAL provides powerful options for aligning reads, selecting alignment methods, and generating detailed reports.

Features

• Multiple Alignment Methods: Choose between naive, regional, and categorical alignment strategies to suit your analysis.
• High Customizability: Adjust parameters such as the number of representative alleles, error tolerance, and paired-read alignment for maximum flexibility.
• Threading Support: Take full advantage of multi-core systems with configurable threading for faster processing.
• Comprehensive Reporting: Generate detailed reports filtered by read, KIR, or allele identifiers.

---

Installation

To use KIRAL, clone this repository, then clone and build minimap2 in the cloned directory, and build the tool:

git clone https://github.com/erfangolpour/KIRAL
cd KIRAL
git clone https://github.com/lh3/minimap2
cd minimap2
make
cd ..
make

---

Usage

1. Align Reads

Use the align command to align sequencing reads to the KIR allele database.

Command:

./main align <database> <reads> [--method <method_name>] [-r <num_representatives>] [--pair] [-t <threads>] [-o <output_file>]

Options:

• <database>: Path to the KIR allele database.
• <reads>: Path to the sequencing reads file.
• --method <method_name>: Alignment method to use. Options are:
  • naive (simple alignment to all alleles),
  • regional (align to representatives for each gene),
  • categorical (align by categorical grouping).
    Default: regional.
• -r <num_representatives>: Number of representative alleles per gene for regional or categorical alignment. Default: 1.
• --pair: Include paired reads in the second pass for regional or categorical alignment.
• -t <threads>: Number of threads to use. Default: Number of hardware threads.
• -o <output_file>: Path to save the alignment results.

2. Analyze Reports

Use the report command to analyze and filter results from a previously generated alignment file.

Command:

./main report <alignments_file> [--head <num_results>] [-r <read_id>] [-k <KIR read_id>] [-a <allele read_id>]

Options:

• <alignments_file>: Path to the file with alignment results.
• --head <num_results>: Display only the first <num_results> alignments.
• -r <read_id>: Show results for a specific read ID.
• -k <KIR read_id>: Show results for a specific KIR ID.
• -a <allele read_id>: Show results for a specific allele ID.

---

Examples

Example 1: Align Reads with Default Settings

./main align KIR_database.fasta reads.fastq -o alignments.txt

Example 2: Use 4 Threads and Pair Alignment

./main align KIR_database.fasta reads.fastq --method regional --pair -t 4 -o paired_alignments.txt

Example 3: Generate a Report for Specific Read ID

./main report alignments.txt -r 12345

Example 4: Show Top 10 Results

./main report alignments.txt --head 10

---

Contributing

Contributions are welcome! Feel free to submit issues or pull requests to improve KIRAL.

---

License

KIRAL is released under the GNU General Public License v3.0.

---

Acknowledgments

Special thanks to:

• The developers of minimap2 for their amazing project. minimap2’s exceptional performance and versatility in sequence alignment have been instrumental in the development of KIRAL.