Pairix

Pairix indexes and queries block-compressed Pairs files containing paired genomic coordinates from Hi-C experiments to enable efficient retrieval of chromosomal interaction data for analysis of spatial genome organization.

Key Features:

• Pairs file format: Provides a specialized block-compressed text file format named Pairs for storing paired genomic coordinates.
• Block compression (bgzipped): Stores data as bgzipped, block-compressed text files to reduce storage while allowing random access.
• Tabix extension: Extends Tabix to handle paired-coordinate data and to support 1D and 2D indexing and querying using genomic coordinates.
• Indexing: Creates indices that enable rapid access to specific genomic regions within Pairs files.
• Implementations: Implemented primarily in C with additional implementations available in Python and R.
• Complementary QC: Includes a complementary tool, PairsQC, that generates collapsible HTML quality-control reports for Pairs files.

Scientific Applications:

• 3D genome architecture analysis: Enables retrieval of Hi-C paired-coordinate data for studies of spatial genome organization.
• Regulatory element interaction mapping: Facilitates targeted access to contact pairs for identification of regulatory element interactions.
• Disease-associated rearrangement studies: Supports investigation of disease-associated genomic rearrangements by providing efficient access to chromosomal interaction data.

Methodology:

Pairix creates an index on bgzipped, block-compressed Pairs files by extending Tabix to perform 1D and 2D indexing and querying of paired genomic coordinates, enabling rapid region-specific access while block compression maintains manageable storage.