Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs

Summary As the amount of three-dimensional chromosomal interaction data continues to increase, storing and accessing such data efficiently becomes paramount. We introduce Pairs, a block-compressed text file format for storing paired genomic coordinates from Hi-C data, and Pairix, an open-source C application to index and query Pairs files. Pairix (also available in Python and R) extends the functionalities of Tabix to paired coordinates data. We have also developed PairsQC, a collapsible HTML quality control report generator for Pairs files. Availability The format specification and source code are available at , and . Contact peter_park{at}hms.harvard.edu or burak_alver{at}hms.harvard.edu ### Competing Interest Statement The authors have declared no competing interest.