Overview

pairtools is a simple and fast command-line framework to process sequencing data from a Hi-C experiment. pairtools perform various operations on Hi-C pairs and occupy the middle position in a typical Hi-C data processing pipeline:

The diagram of a typical processing pipeline for Hi-C data

In a typical Hi-C pipeline, DNA sequences (reads) are aligned to the reference genome, converted into ligation junctions and binned, thus producing a Hi-C contact map.

pairtools aim to be an all-in-one tool for processing Hi-C pairs, and can perform 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

pairtools produce .pairs files compliant with the 4DN standard.

pairtools uses a two-character notation to define pair types (see table _section-pair-types)

The full list of available pairtools:

Pairtool

Description

dedup

Find and remove PCR/optical duplicates.

filterbycov

Remove pairs from regions of high coverage.

flip

Flip pairs to get an upper-triangular matrix.

markasdup

Tag pairs as duplicates.

merge

Merge sorted .pairs/.pairsam files.

parse

Find ligation junctions in .sam, make .pairs.

phase

Phase pairs mapped to a diploid genome.

restrict

Assign restriction fragments to pairs.

select

Select pairs according to some condition.

sort

Sort a .pairs/.pairsam file.

split

Split a .pairsam file into .pairs and .sam.

stats

Calculate pairs statistics.

Contents:

Tutorials