python-pairtools 0.3.0 Process mapped Hi-C data

Pairtools is a simple and fast command-line framework to process sequencing data from a Hi-C experiment. Process pair-end sequence alignments and perform the following operations:

  • detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end sequences of Hi-C DNA molecules

  • sort .pairs files 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 .sam alignments from Hi-C pairs.