pgltools

pgltools provides a suite of operations and a file standard for manipulating paired-genomic-loci (PGL) interaction data from next-generation sequencing (NGS) studies to support analysis of chromosomal interactions.

Key Features:

• Paired-Genomic-Loci (PGL) file standard: A standardized format for representing paired genomic loci interactions generated by NGS-based chromatin interaction assays.
• Annotation operations: Functions to annotate PGL interactions with genomic features.
• Intersection operations: Functions to compute overlaps between PGL datasets from different experiments.
• Merging operations: Functions to merge multiple PGL interaction datasets into combined outputs.
• Python module integration: A Python module interface for incorporation into bioinformatics pipelines.
• Cross-platform and pypy compatibility: Executable across operating systems and compatible with pypy for improved runtime performance.

Scientific Applications:

• Genomic interaction analysis: Analysis of chromosomal interactions from PGL data produced by NGS chromatin interaction experiments.
• Gene regulation studies: Linking PGL interactions to regulatory elements to investigate gene regulation mechanisms.
• Chromatin organization and spatial genome architecture: Characterizing chromatin organization and spatial relationships between loci.
• Comparative analyses across experiments: Annotating, intersecting, and merging interaction datasets from multiple experiments for comparative studies.

Methodology:

Operations use the paired-genomic-loci (PGL) file standard to perform data manipulation tasks including annotation, intersection, and merging of PGL datasets.