Metadata-Version: 2.4
Name: split3c
Version: 0.0.2
Summary: Toolkit to split and resolve chimeric 3C/Hi-C/Micro-C reads
Author-email: Samir Bertache <samir.bertache.djenadi@gmail.com>
License-Expression: AGPL-3.0-or-later
Project-URL: Homepage, https://gitbio.ens-lyon.fr/LBMC/physbio/split3c
Project-URL: Documentation, https://gitbio.ens-lyon.fr/LBMC/physbio/split3c/-/wikis/Home
Project-URL: Repository, https://gitbio.ens-lyon.fr/LBMC/physbio/split3c
Keywords: Hi-C,Micro-C,3C,bioinformatics,chimeric reads
Requires-Python: >=3.12
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: biopython>=1.83
Requires-Dist: pysam>=0.23.3
Requires-Dist: rich>=14.3.3
Requires-Dist: rich-argparse>=1.7.2
Provides-Extra: dev
Requires-Dist: pytest>=9.0.2; extra == "dev"
Requires-Dist: pytest-cov>=7.0.0; extra == "dev"
Requires-Dist: coverage[toml]; extra == "dev"
Requires-Dist: build>=1.2.0; extra == "dev"
Requires-Dist: twine>=5.0.0; extra == "dev"
Dynamic: license-file

[![pipeline status](https://gitbio.ens-lyon.fr/LBMC/physbio/split3c/badges/master/pipeline.svg)](https://gitbio.ens-lyon.fr/LBMC/physbio/split3c/-/pipelines)
[![coverage report](https://gitbio.ens-lyon.fr/LBMC/physbio/split3c/badges/master/coverage.svg?job=tests)](https://gitbio.ens-lyon.fr/LBMC/physbio/split3c/-/commits/main)

# `split3c`

`split3c` is a toolkit for preprocessing 3C-type sequencing libraries and converting BAM alignments into `.pairs` files for chromatin contact analysis.

It provides three main subcommands:

- `split3c re-site`
- `split3c ns-site`
- `split3c resolve`

Full documentation is available in the wiki:

- [Wiki home](https://gitbio.ens-lyon.fr/LBMC/physbio/split3c/-/wikis/Home)
- [Installation](https://gitbio.ens-lyon.fr/LBMC/physbio/split3c/-/wikis/Installation)
- [Quick start](https://gitbio.ens-lyon.fr/LBMC/physbio/split3c/-/wikis/Quick-start)
- [Overview](https://gitbio.ens-lyon.fr/LBMC/physbio/split3c/-/wikis/Overview)
- [Examples](https://gitbio.ens-lyon.fr/LBMC/physbio/split3c/-/wikis/Examples)
- [Troubleshooting](https://gitbio.ens-lyon.fr/LBMC/physbio/split3c/-/wikis/Troubleshooting)

---

## Installation

```bash
pip install split3c
````

Or in development mode:

```bash
pip install -e .
```

Quick checks:

```bash
split3c --help
split3c re-site --help
split3c ns-site --help
split3c resolve --help
```

---

## Main workflows

### `split3c re-site`

Restriction enzyme-based workflow for Hi-C / HiChIP / 3C-like libraries.

![split3c re-site workflow](doc/img/resite-workflow.png)

---

### `split3c ns-site`

Non-specific ligation workflow for Micro-C-like libraries.

![split3c ns-site workflow](doc/img/nssite-workflow.png)

---

## Benchmark

![split3c benchmark](doc/img/benchmark.png)

---

## License

split3c is released under the AGPLv3 license.
