Pairtools: From sequencing data to chromosome contacts

The field of 3D genome organization produces large amounts of sequencing data from Hi-C and a rapidly-expanding set of other chromosome conformation protocols (3C+). Massive and heterogeneous 3C+ data require high-performance and flexible processing of sequenced reads into contact pairs. To meet these challenges, we present pairtools-a flexible suite of tools for contact extraction from sequencing data. Pairtools provides modular command-line interface (CLI) tools that can be flexibly chained into data processing pipelines. The core operations provided by pairtools are parsing of.sam alignments into Hi-C pairs, sorting and removal of PCR duplicates. In addition, pairtools provides auxiliary tools for building…

• ÖA
  Österreichischen Akademie der Wissenschaften
• AS
  Austrian Science Fund
• NI
  National Institutes of Health

  Awards: R01 HG003143, R35 GM143116-01, UM1-HG011536, 17-00-00180, HG003143, HG011536
• CF
  Common Fund