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OptiType Specifications

Process Details

  • Name: OptiType
  • Process UUID: dgfbb98mgdbyp7aiqg8vjrpqt0ap77
  • Process Group: HLA

Overview

OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles. This process enables precise identification of human leukocyte antigen (HLA) types from sequencing data, which is crucial for transplantation compatibility, disease association studies, and personalized medicine applications.

This process is implemented in Bash, which invokes the OptiTypePipeline.py script for HLA genotyping analysis.

Key Functionality

  • HLA Class I Genotyping: Performs accurate 4-digit HLA-A, HLA-B, and HLA-C genotyping from NGS data
  • Integer Linear Programming: Uses advanced optimization algorithms to simultaneously select all major and minor HLA alleles
  • Multi-format Support: Processes both DNA and RNA sequencing data with appropriate parameter settings
  • Comprehensive Output: Generates detailed results including genotyping predictions, confidence scores, and visualization reports

Input/Output Specification

Inputs

Required Inputs

  • Sequencing Reads

    • Description: NGS sequencing data files containing reads for HLA genotyping analysis
    • Format: FASTQ

  • Mate Information

    • Description: Mate pair information for paired-end sequencing data
    • Format: mate

Outputs

  • HLA Genotyping Results

    • Description: Detailed HLA genotyping predictions with allele assignments and confidence scores
    • Format: CSV

  • Visualization Report

    • Description: Graphical representation of HLA genotyping results and coverage plots
    • Format: PDF

  • Alignment File

    • Description: Aligned reads used for HLA genotyping analysis
    • Format: BAM

Parameters & Settings

These parameters can be adjusted in the Foundry UI when running this process.

  • Sequencing Data Type
    • Description: Type of sequencing data to analyze for HLA genotyping
    • Available options: dna, rna (default)

References & Resources

  • Tool Documentation: Contact the team for details on OptiTypePipeline.py
  • Related Papers: Szolek, A., Schubert, B., Mohr, C., Sturm, M., Feldhahn, M., & Kohlbacher, O. (2014). OptiType: precision HLA typing from next-generation sequencing data. Bioinformatics, 30(23), 3310-3316. DOI: 10.1093/bioinformatics/btu548