pairtools

pairtools extracts and processes chromosome contact pairs from sequencing data generated by Hi-C and related chromosome conformation capture (3C+) protocols.

Key Features:

• Contact Parsing: Parses .sam alignments into Hi-C pairs.
• Sorting and Deduplication: Sorts contact pairs and removes PCR duplicates.
• Contact Manipulation: Provides tools for contact pair manipulation and filtration.
• Quality Control: Includes quality control functionality for 3C+ data.
• Protocol-Specific Tools: Provides tools for restriction-based protocols, haplotype-resolved contacts, and single-cell Hi-C.
• Pipeline Integration: Modular command-line tools can be chained into data processing pipelines and integrate with Python data analysis libraries.

Scientific Applications:

• Hi-C Data Analysis: Processes sequencing data from Hi-C experiments into chromosome contact pairs.
• 3C+ Protocol Analysis: Supports a broad range of chromosome conformation capture protocols beyond standard Hi-C.
• Haplotype-Resolved Analysis: Enables extraction of haplotype-resolved chromosome contacts.
• Single-Cell Hi-C: Processes contact data from single-cell Hi-C experiments.

Methodology:

pairtools uses modular command-line tools that parse .sam alignments into Hi-C pairs, with core operations including sorting and PCR duplicate removal.