Work

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

Year: 2021

Type: article

Abstract: 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.

Source: Bioinformatics

DOI: 10.1093/bioinformatics/btab870

Authors: Soohyun Lee, Clara R Bakker, Carl Vitzthum, Burak H Alver, Peter J Park

Institution: Harvard University

Language: English

Topic: Genomics and Chromatin Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: bronze

Funders: National Institutes of Health, National Cancer Institute, Common Fund

Award: 4D Nucleome Network Data Coordination and Integration Center