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Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs
Soohyun Lee1, Clara R Bakker1, Carl Vitzthum1
1Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
Summary:
As the amount of 3D 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 And Implementation:
The 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.
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