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.
- Parsing alignments into pairs
- .pairsam format
- Command-line tools