Description

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

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