pairsamtools¶
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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