| Name | seqspec JSON |
| Version |
0.4.0
JSON |
| download |
| home_page | None |
| Summary | A tool for working with sequencing specifications |
| upload_time | 2025-08-25 23:28:24 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.12 |
| license | MIT |
| keywords |
bioinformatics
sequencing
specifications
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# seqspec
[](https://pypi.org/project/seqspec/0.4.0/)
[](LICENSE)
`seqspec`, short for "sequence specification" (pronounced "seek-speck"), is a file format that describes data generated from genomics experiments. Both the file format and `seqspec` tool [enable uniform processing](./docs/UNIFORM.md) of genomics data.
**Figure 1**: Anatomy of a `seqspec` file.
We have multiple tutorials to get you up and running with `seqspec`:
1. Learn how to use `seqspec` to [standardize your genomics data preprocessing](docs/UNIFORM.ipynb).
2. Understand how to [manipulate `seqspec` files](docs/USING_SEQSPEC.ipynb) using the `seqspec` command-line tool.
## Citation
The `seqspec` format and tool are described in this [publication](https://doi.org/10.1093/bioinformatics/btae168). If you use `seqspec` please cite
```
Ali Sina Booeshaghi, Xi Chen, Lior Pachter, A machine-readable specification for genomics assays, Bioinformatics, Volume 40, Issue 4, April 2024, btae168.
```
`seqspec` was inspired by and builds off of the Teichmann Lab [Single Cell Genomics Library Structure](https://github.com/Teichlab/scg_lib_structs) by [Xi Chen](https://github.com/dbrg77).
## Documentation
- [Install `seqspec`: `docs/INSTALLATION.md`](docs/INSTALLATION.md)
- [Learn about the `seqspec` file format: `docs/DOCUMENTATION.md`](docs/SEQSPEC_FILE.md)
- [Learn about the `seqspec` tool: `docs/DOCUMENTATION.md`](docs/SEQSPEC_TOOL.md)
- [Learn about the `seqspec` specification : `docs/SPECIFICATION.md`](docs/SPECIFICATION.md)
- [Write a `seqspec`: `docs/TUTORIAL.md`](docs/TUTORIAL.md)
- [View example `seqspec` files: `https://www.sina.bio/seqspec-builder/assays.html`](https://www.sina.bio/seqspec-builder/assays.html)
- [Contribute a `seqspec` : `docs/CONTRIBUTING.md`](docs/CONTRIBUTING.md)
- [Watch a YouTube video about `seqspec`](https://youtu.be/NSj6Vpzy8tU)
- [Read the manuscript that describes `seqspec`](https://doi.org/10.1093/bioinformatics/btae168)
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"description": "# seqspec\n\n\n[](https://pypi.org/project/seqspec/0.4.0/)\n\n[](LICENSE)\n\n`seqspec`, short for \"sequence specification\" (pronounced \"seek-speck\"), is a file format that describes data generated from genomics experiments. Both the file format and `seqspec` tool [enable uniform processing](./docs/UNIFORM.md) of genomics data.\n\n\n**Figure 1**: Anatomy of a `seqspec` file.\n\nWe have multiple tutorials to get you up and running with `seqspec`:\n\n1. Learn how to use `seqspec` to [standardize your genomics data preprocessing](docs/UNIFORM.ipynb).\n\n2. Understand how to [manipulate `seqspec` files](docs/USING_SEQSPEC.ipynb) using the `seqspec` command-line tool.\n\n## Citation\n\nThe `seqspec` format and tool are described in this [publication](https://doi.org/10.1093/bioinformatics/btae168). If you use `seqspec` please cite\n\n```\nAli Sina Booeshaghi, Xi Chen, Lior Pachter, A machine-readable specification for genomics assays, Bioinformatics, Volume 40, Issue 4, April 2024, btae168.\n```\n\n`seqspec` was inspired by and builds off of the Teichmann Lab [Single Cell Genomics Library Structure](https://github.com/Teichlab/scg_lib_structs) by [Xi Chen](https://github.com/dbrg77).\n\n## Documentation\n\n- [Install `seqspec`: `docs/INSTALLATION.md`](docs/INSTALLATION.md)\n- [Learn about the `seqspec` file format: `docs/DOCUMENTATION.md`](docs/SEQSPEC_FILE.md)\n- [Learn about the `seqspec` tool: `docs/DOCUMENTATION.md`](docs/SEQSPEC_TOOL.md)\n- [Learn about the `seqspec` specification : `docs/SPECIFICATION.md`](docs/SPECIFICATION.md)\n- [Write a `seqspec`: `docs/TUTORIAL.md`](docs/TUTORIAL.md)\n- [View example `seqspec` files: `https://www.sina.bio/seqspec-builder/assays.html`](https://www.sina.bio/seqspec-builder/assays.html)\n- [Contribute a `seqspec` : `docs/CONTRIBUTING.md`](docs/CONTRIBUTING.md)\n- [Watch a YouTube video about `seqspec`](https://youtu.be/NSj6Vpzy8tU)\n- [Read the manuscript that describes `seqspec`](https://doi.org/10.1093/bioinformatics/btae168)\n",
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