Pairs and Pairix: a file format and a tool for efficient storage and retrieval for Hi-C read pairs.
basic_science · Level V
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- Record sourced from PubMed, PMID 34978573.
- Also identified by DOI 10.1093/bioinformatics/btab870 and PMC identifier 10060703.
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Abstract
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. 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.
Medical subject headings
- Software
- Genomics