{"id":39491833,"url":"https://github.com/openomics/nanite","last_synced_at":"2026-01-18T05:36:55.624Z","repository":{"id":115513090,"uuid":"578672324","full_name":"OpenOmics/nanite","owner":"OpenOmics","description":"A streamlined Oxford Nanopore Viral Metagenomics Pipeline ","archived":false,"fork":false,"pushed_at":"2025-03-27T19:53:22.000Z","size":642,"stargazers_count":4,"open_issues_count":1,"forks_count":2,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-09-04T23:50:43.401Z","etag":null,"topics":["annotation","assembly","classification","pathogen-surveillance","pipeline","singularity","slim","snakemake","viral-metagenomics"],"latest_commit_sha":null,"homepage":"https://openomics.github.io/nanite","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/OpenOmics.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2022-12-15T15:56:05.000Z","updated_at":"2025-03-27T19:52:42.000Z","dependencies_parsed_at":null,"dependency_job_id":"e7338977-6c08-47d2-ac51-b257e3b9c682","html_url":"https://github.com/OpenOmics/nanite","commit_stats":{"total_commits":56,"total_committers":1,"mean_commits":56.0,"dds":0.0,"last_synced_commit":"1cc39b6855a19ec5810ef2bd4c2bed4935b849c0"},"previous_names":[],"tags_count":13,"template":false,"template_full_name":"OpenOmics/baseline","purl":"pkg:github/OpenOmics/nanite","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenOmics%2Fnanite","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenOmics%2Fnanite/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenOmics%2Fnanite/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenOmics%2Fnanite/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/OpenOmics","download_url":"https://codeload.github.com/OpenOmics/nanite/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/OpenOmics%2Fnanite/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28530988,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-18T00:39:45.795Z","status":"online","status_checked_at":"2026-01-18T02:00:07.578Z","response_time":98,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":["annotation","assembly","classification","pathogen-surveillance","pipeline","singularity","slim","snakemake","viral-metagenomics"],"created_at":"2026-01-18T05:36:54.955Z","updated_at":"2026-01-18T05:36:55.614Z","avatar_url":"https://github.com/OpenOmics.png","language":"Python","readme":"\u003cdiv align=\"center\"\u003e\n   \n  \u003ch1\u003enanite 🔬\u003c/h1\u003e\n  \n  **_Viral Nanopore Pipeline_**\n\n  [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7477631.svg)](https://doi.org/10.5281/zenodo.7477631) [![GitHub release (latest SemVer including pre-releases)](https://img.shields.io/github/v/release/OpenOmics/nanite?color=blue\u0026include_prereleases)](https://github.com/OpenOmics/nanite/releases) [![Docker Pulls](https://img.shields.io/docker/pulls/skchronicles/nanite)](https://hub.docker.com/repository/docker/skchronicles/nanite)\u003cbr\u003e[![tests](https://github.com/OpenOmics/nanite/workflows/tests/badge.svg)](https://github.com/OpenOmics/nanite/actions/workflows/main.yaml) [![docs](https://github.com/OpenOmics/nanite/workflows/docs/badge.svg)](https://github.com/OpenOmics/nanite/actions/workflows/docs.yml) [![GitHub issues](https://img.shields.io/github/issues/OpenOmics/nanite?color=brightgreen)](https://github.com/OpenOmics/nanite/issues)  [![GitHub license](https://img.shields.io/github/license/OpenOmics/nanite)](https://github.com/OpenOmics/nanite/blob/main/LICENSE) \n  \n  \u003ci\u003e\n    This is the home of the pipeline, nanite. Its long-term goals: to assemble, annotate, and screen nanopore samples like no pipeline before!\n  \u003c/i\u003e\n\u003c/div\u003e\n\n## Overview\nWelcome to nanite! Before getting started, we highly recommend reading through [nanite's documentation](https://openomics.github.io/nanite/).\n\nThe **`./nanite`** pipeline is composed several inter-related sub commands to setup and run the pipeline across different systems. Each of the available sub commands perform different functions: \n\n * [\u003ccode\u003enanite \u003cb\u003erun\u003c/b\u003e\u003c/code\u003e](https://openomics.github.io/nanite/usage/run/): Run the nanite pipeline with your input files.\n * [\u003ccode\u003enanite \u003cb\u003eunlock\u003c/b\u003e\u003c/code\u003e](https://openomics.github.io/nanite/usage/unlock/): Unlocks a previous runs output directory.\n * [\u003ccode\u003enanite \u003cb\u003einstall\u003c/b\u003e\u003c/code\u003e](https://openomics.github.io/nanite/usage/install/): Download reference files locally.\n * [\u003ccode\u003enanite \u003cb\u003ecache\u003c/b\u003e\u003c/code\u003e](https://openomics.github.io/nanite/usage/cache/): Cache software containers locally.\n\n**nanite** is a streamlined viral metagenomics pipeline to assemble, annotate, and classify microorganisms in enviromental samples. It relies on technologies like [Singularity\u003csup\u003e1\u003c/sup\u003e](https://singularity.lbl.gov/) to maintain the highest-level of reproducibility. The pipeline consists of a series of data processing and quality-control steps orchestrated by [Snakemake\u003csup\u003e2\u003c/sup\u003e](https://snakemake.readthedocs.io/en/stable/), a flexible and scalable workflow management system, to submit jobs to a cluster.\n\nThe pipeline is compatible with data generated from [Nanopore sequencing technologies](https://nanoporetech.com/). As input, it accepts a set of FastQ files and can be run locally on a compute instance or on-premise using a cluster. A user can define the method or mode of execution. The pipeline can submit jobs to a cluster using a job scheduler like SLURM (more coming soon!). A hybrid approach ensures the pipeline is accessible to all users.\n\nBefore getting started, we highly recommend reading through the [usage](https://openomics.github.io/nanite/usage/run/) section of each available sub command.\n\nFor more information about issues or trouble-shooting a problem, please checkout our [FAQ](https://openomics.github.io/nanite/faq/questions/) prior to [opening an issue on Github](https://github.com/OpenOmics/nanite/issues).\n\n## Dependencies\n**Requires:** `singularity\u003e=3.5`  `snakemake\u003e=6.0`  `conda/mamba (optional)` \n\n[Snakemake](https://snakemake.readthedocs.io/en/stable/getting_started/installation.html) must be installed on the target system. Snakemake is a workflow manager that orchestrates each step of the pipeline. The second dependency, i.e [singularity](https://singularity.lbl.gov/all-releases) OR [conda/mamba](https://github.com/conda-forge/miniforge#mambaforge), handles the dowloading/installation of any remaining software dependencies. By default, the pipeline will utilize singularity to guarantee the highest level of reproducibility; however, the `--use-conda` option of the [run](https://openomics.github.io/nanite/usage/run/) sub command can be provided to  use conda/mamba instead of singularity. If possible, we recommend using singularity over conda for reproducibility; however, it is worth noting that singularity and conda produce identical results for this pipeline. \n\nIf you are running the pipeline on Windows, please use the [Windows Subsystem for Linux (WSL)](https://learn.microsoft.com/en-us/windows/wsl/install). Singularity can be installed on WSL following these [instructions](https://www.blopig.com/blog/2021/09/using-singularity-on-windows-with-wsl2/).\n\n## Installation\nPlease clone this repository to your local filesystem using the following command:\n```bash\n# Clone Repository from Github\ngit clone https://github.com/OpenOmics/nanite.git\n# Change your working directory\ncd nanite/\n# Add dependencies to $PATH\n# Biowulf users should run\nmodule load snakemake singularity\n# Get usage information\n./nanite -h\n```\n\nFor more detailed installation instructions, please see our [setup page](https://openomics.github.io/nanite/setup/).\n\n## Contribute \nThis site is a living document, created for and by members like you. nanite is maintained by the members of OpenOmics and is improved by continous feedback! We encourage you to contribute new content and make improvements to existing content via pull request to our [GitHub repository](https://github.com/OpenOmics/nanite).\n\n## Cite\n\nIf you use this software, please cite it as below:  \n\n\u003cdetails\u003e\n  \u003csummary\u003e\u003cb\u003e\u003ci\u003e@BibText\u003c/i\u003e\u003c/b\u003e\u003c/summary\u003e\n \n```text\n@software{Kuhn_OpenOmics_nanite_2022,\n  author = {Skyler Kuhn and Paul Schaughency},\n  doi    = {10.5281/zenodo.7477631},\n  title  = {OpenOmics/nanite},\n  month  = dec,\n  year   = 2022,\n  url    = {https://github.com/OpenOmics/nanite/}\n}\n```\n\n\u003c/details\u003e\n\n\u003cdetails\u003e\n  \u003csummary\u003e\u003cb\u003e\u003ci\u003e@APA\u003c/i\u003e\u003c/b\u003e\u003c/summary\u003e\n\n```text\nSkyler Kuhn, \u0026 Paul Schaughency. (2022). OpenOmics/nanite [Computer software]. https://doi.org/10.5281/zenodo.7477631\n```\n\n\u003c/details\u003e\n\nFor more citation style options, please visit the pipeline's [Zenodo page](https://doi.org/10.5281/zenodo.7477631).\n\n## References\n\u003csup\u003e**1.**  Kurtzer GM, Sochat V, Bauer MW (2017). Singularity: Scientific containers for mobility of compute. PLoS ONE 12(5): e0177459.\u003c/sup\u003e  \n\u003csup\u003e**2.**  Koster, J. and S. Rahmann (2018). \"Snakemake-a scalable bioinformatics workflow engine.\" Bioinformatics 34(20): 3600.\u003c/sup\u003e  \n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenomics%2Fnanite","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fopenomics%2Fnanite","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenomics%2Fnanite/lists"}