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:
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