PRINCESS

PRINCESS performs integrated variant calling, methylation detection, and phasing from raw FASTA or FASTQ reads to produce a comprehensive, phased set of single-nucleotide variants (SNVs), structural variants (SVs), and methylation calls for genomic analysis.

Key Features:

• Integrated Variant Analysis: Combines SNV, SV, and methylation analyses to deliver a holistic view of genomic variation within a sample.
• High Accuracy and Long Phasing: Achieves high accuracy in variant calling and maintains long phasing lengths even with low-coverage datasets.
• Efficient Handling of Complex Genes: Resolves medically relevant genes that are repetitive or structurally complex.
• Scalability and Speed: Utilizes cluster environments to accelerate processing from raw FASTA/FASTQ reads and can generate a fully phased call set within hours.
• Comprehensive Outputs: Produces phased SNVs, SVs, and methylation calls as primary outputs.

Scientific Applications:

• Genetic diversity and population genomics: Enables studies of genetic variation and population-level diversity using phased variant and methylation data.
• Disease mechanism and clinical genetics: Supports investigation of disease mechanisms and analysis of medically relevant, complex genomic regions.
• Therapeutic target discovery and personalized medicine: Facilitates identification of therapeutic targets and applications in personalized medicine through comprehensive phased variant and methylation profiling.

Methodology:

Processes raw FASTA/FASTQ reads to perform variant calling (SNVs and SVs), methylation calling, and phasing, using cluster environments to accelerate computation and produce fully phased call sets.