PT  - JOURNAL ARTICLE
AU  - Soohyun Lee
AU  - Carl Vitzthum
AU  - Burak H. Alver
AU  - Peter J. Park
TI  - Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs
AID  - 10.1101/2021.08.24.457552
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.08.24.457552
4099  - http://biorxiv.org/content/early/2021/08/26/2021.08.24.457552.short
4100  - http://biorxiv.org/content/early/2021/08/26/2021.08.24.457552.full
AB  - 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 https://github.com/4dn-dcic/pairix, https://github.com/4dn-dcic/Rpairix and https://github.com/4dn-dcic/pairsqc.Contact peter_park{at}hms.harvard.edu or burak_alver{at}hms.harvard.eduCompeting Interest StatementThe authors have declared no competing interest.