HemoMIPs-Automated analysis and result reporting pipeline for targeted sequencing data

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Targeted sequencing offers a cost-effective method for patient cohort screening.
• Analyzing highly imbalanced next-generation sequencing data, particularly from molecular inversion probes (MIPs), presents computational challenges.

Purpose of the Study:

• To develop and present a fast and efficient bioinformatics pipeline for analyzing targeted next-generation sequencing data generated by MIP capture.
• To provide a comprehensive analysis workflow that includes variant calling, coverage analysis, and report generation for genetic screening.

Main Methods:

• A Snakemake-based pipeline was developed for automated analysis.
• The workflow includes sample demultiplexing, paired-end merging, alignment, MIP-arm trimming, variant calling, and coverage analysis.
• The pipeline supports structural variant analysis and sex assignment using specific probes.

Main Results:

• The HemoMIPs pipeline successfully processes and analyzes targeted sequencing data.
• It generates a user-friendly HTML report summarizing key findings, including variants, their effects, and region coverage.
• The pipeline was validated using the hemophilia A & B MIP design.

Conclusions:

• HemoMIPs provides a robust and efficient solution for analyzing MIP-based targeted sequencing data.
• The open-source tool facilitates genetic screening and variant analysis in patient cohorts.
• This workflow enhances the utility of targeted sequencing for genetic studies.