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bioRxiv · 10.1101/2021.08.24.457552

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

Lee, S.·Vitzthum, C.·Alver, B. H.·Park, P. J.
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Abstract

SummaryAs 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. AvailabilityThe format specification and source code are available at https://github.com/4dn-dcic/pairix, https://github.com/4dn-dcic/Rpairix and https://github.com/4dn-dcic/pairsqc. Contactpeter_park@hms.harvard.edu or burak_alver@hms.harvard.edu

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Lee, S., Vitzthum, C., Alver, B. H., Park, P. J.. 2021-08-26. Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs. https://doi.org/10.1101/2021.08.24.457552

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