pairsamtools is a set of simple and fast command-line tools to process sequencing data from Hi-C experiments.

pairsamtools operate on sequence alignments and perform the following operations:

  • detect and classify ligation sites (a.k.a. Hi-C pairs) produced in Hi-C experiments
  • sort Hi-C pairs for downstream analyses
  • detect, tag and remove PCR/optical duplicates
  • generate extensive statistics of Hi-C datasets
  • select Hi-C pairs given flexibly defined criteria
  • restore and tag .sam files for selected subsets of Hi-C pairs

pairsamtools produce .pairs files compliant with the 4DN standards.


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