title: Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data.
abstract: BACKGROUND
  Genomic interaction studies use next-generation sequencing (NGS) to examine the interactions between two loci on the genome, with subsequent bioinformatics analyses typically including annotation, intersection, and merging of data from multiple experiments. While many file types and analysis tools exist for storing and manipulating single locus NGS data, there is currently no file standard or analysis tool suite for manipulating and storing paired-genomic-loci: the data type resulting from "genomic interaction" studies. As genomic interaction sequencing data are becoming prevalent, a standard file format and tools for working with these data conveniently and efficiently are needed.
  
  
  RESULTS
  This article details a file standard and novel software tool suite for working with paired-genomic-loci data. We present the paired-genomic-loci (PGL) file standard for genomic-interactions data, and the accompanying analysis tool suite "pgltools": a cross platform, pypy compatible python package available both as an easy-to-use UNIX package, and as a python module, for integration into pipelines of paired-genomic-loci analyses.
  
  
  CONCLUSIONS
  Pgltools is a freely available, open source tool suite for manipulating paired-genomic-loci data. Source code, an in-depth manual, and a tutorial are available publicly at www.github.com/billgreenwald/pgltools , and a python module of the operations can be installed from PyPI via the PyGLtools module.
authors.affiliation: Bioinformatics and Systems Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
authors.forename: William W
authors.initials: WW
authors.lastname: Greenwald
authors.affiliation: Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.|Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
authors.forename: He
authors.initials: H
authors.lastname: Li
authors.affiliation: Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
authors.forename: Erin N
authors.initials: EN
authors.lastname: Smith
authors.affiliation: Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
authors.forename: Paola
authors.initials: P
authors.lastname: Benaglio
authors.affiliation: Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.|Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
authors.forename: Naoki
authors.initials: N
authors.lastname: Nariai
authors.affiliation: Institute for Genomic Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. kafrazer@ucsd.edu.|Department of Pediatrics and Rady Children's Hospital, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA. kafrazer@ucsd.edu.
authors.forename: Kelly A
authors.initials: KA
authors.lastname: Frazer
mesh_terms: D002843:Chromatin / Q000235:genetics / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D056426:Genetic Loci; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D012984:Software
chemical_list: D002843:Chromatin
keywords: Bedtools; Chromatin conformation capture; Genomic arithmetic; Hi-CChIA-PET; Paired-genomic-loci; Peak; Tool suite