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
.pairsfiles 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
.samalignments from Hi-C pairs.