{"id":25596867,"url":"https://github.com/nanoporetech/ont-spectre","last_synced_at":"2025-07-19T11:07:06.692Z","repository":{"id":238684611,"uuid":"797242577","full_name":"nanoporetech/ont-spectre","owner":"nanoporetech","description":null,"archived":false,"fork":false,"pushed_at":"2024-11-08T11:56:26.000Z","size":83966,"stargazers_count":6,"open_issues_count":6,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-04-06T08:02:15.262Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/nanoporetech.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2024-05-07T13:17:14.000Z","updated_at":"2025-03-09T08:04:26.000Z","dependencies_parsed_at":null,"dependency_job_id":"d20ed844-bf80-49c0-b5b5-a107c4df33bf","html_url":"https://github.com/nanoporetech/ont-spectre","commit_stats":null,"previous_names":["epi2me-labs/ont-spectre"],"tags_count":6,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Font-spectre","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Font-spectre/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Font-spectre/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Font-spectre/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nanoporetech","download_url":"https://codeload.github.com/nanoporetech/ont-spectre/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248657795,"owners_count":21140841,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2025-02-21T12:34:58.409Z","updated_at":"2025-04-13T02:31:50.753Z","avatar_url":"https://github.com/nanoporetech.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"![Spectre](./logo.png)\n\n# Spectre - Long-read CNV Caller\n\n[Spectre](https://github.com/fritzsedlazeck/Spectre/tree/main) is a long-read copy number variation (CNV) caller designed to detect large CNVs (\u003e100kb).\n\n**Ont-spectre** is a tool based on the original Spectre v0.2.0, with the following main enhancements:\n* **Diploid Coverage Estimation:** Bins containing heterozygous SNVs are used to estimate the properties of the diploid coverage distribution, aiding in the selection of appropriate parameters.\n* **Karyotype Prediction:** Adds sex chromosome karyotype prediction (including XO, XXY, etc). All events are called relative to the predicted karyotype.\n\n## Installation\n\nThe recommended way to install Spectre is through either `pip` or `conda`:\n\n```bash\npip install ont-spectre\n\n```\n(or)\n```bash\nconda install nanoporetech::ont-spectre\n```\n\n\u003e **Note**: Spectre supports Python versions \u003e= 3.8.\n\n## Build from Source\n\nTo install the `ont-spectre` tool from the source, follow these steps:\n\n1. **Clone the repository:**\n\n   ```bash\n   git clone https://github.com/epi2me-labs/ont-spectre.git\n   cd ont-spectre\n   ```\n\n2. **Create a virtual environment (optional):**\n\n   It’s recommended to use a isolated environment to manage dependencies. Create and activate one with:\n\n   ```bash\n   python3 -m venv venv\n   source venv/bin/activate  # On Windows: venv\\Scripts\\activate\n   ```\n\n   Alternatively, you can create a conda environment:\n\n   ```bash\n   conda create -n spectre python=3.8 pip -y\n   conda activate spectre\n   ```\n\n\u003e **Note**: Spectre supports Python versions \u003e= 3.8.\n\n3. **Install dependencies and the tool:**\n\n   ```bash\n   pip install .\n   ```\n\n4. **Verify installation:**\n\n   After installation, you should be able to run the tool using the entry point `spectre`:\n\n   ```bash\n   spectre --help\n   ```\n\n## How to run\n\nSpectre requires the following inputs:\n- The output directory of [mosdepth](https://github.com/brentp/mosdepth), a tool for fast coverage calculation.\n- The reference genome (can be bgzip-compressed).\n- The window size used in Mosdepth (Ensure that the binsize between Mosdepth and Spectre matches. We suggest a binsize of 1,000 base pairs).\n- A VCF file containing SNVs (Single Nucleotide Variants).\n\n### Example Command:\n\n```bash\nspectre CNVCaller \\\n  --bin-size 1000 \\\n  --coverage mosdepth/sampleid/ \\\n  --sample-id sampleid \\\n  --output-dir sampleid_output_directory_path/ \\\n  --reference reference.fasta.gz \\\n  --snv sampleid.vcf.gz\n```\n\n## Help\n\n**Licence and Copyright**\n\n© 2024- Oxford Nanopore Technologies Ltd.\n\n`ont-spectre` is distributed under the terms of the Oxford Nanopore Technologies Public License v1.0.\n\n**Research Release**\n\nResearch releases are provided as technology demonstrators to provide early\naccess to features or stimulate Community development of tools. Support for\nthis software will be minimal and is only provided directly by the developers.\nFeature requests, improvements, and discussions are welcome and can be\nimplemented by forking and pull requests. However much as we would\nlike to rectify every issue and piece of feedback users may have, the\ndevelopers may have limited resource for support of this software. Research\nreleases may be unstable and subject to rapid iteration by Oxford Nanopore\nTechnologies.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnanoporetech%2Font-spectre","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnanoporetech%2Font-spectre","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnanoporetech%2Font-spectre/lists"}