{"id":40545008,"url":"https://github.com/mooreryan/zetahunter","last_synced_at":"2026-01-20T23:36:32.268Z","repository":{"id":152654451,"uuid":"49095950","full_name":"mooreryan/ZetaHunter","owner":"mooreryan","description":"Reproducible taxonomic classification for Zetaproteobacteria and other poorly resolved taxa.","archived":false,"fork":false,"pushed_at":"2018-11-19T19:58:53.000Z","size":40582,"stargazers_count":3,"open_issues_count":10,"forks_count":2,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-10-10T17:14:52.272Z","etag":null,"topics":["classification","otus","ssu-rrna","taxonomy","zetaproteobacteria"],"latest_commit_sha":null,"homepage":"http://dx.doi.org/10.1128/MRA.00932-18","language":"Ruby","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mooreryan.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"COPYING","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"citation/zeta_hunter.bib","codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2016-01-05T22:12:52.000Z","updated_at":"2021-03-07T15:27:35.000Z","dependencies_parsed_at":null,"dependency_job_id":"72e28862-89f0-46b6-acd1-d55735ca3fc9","html_url":"https://github.com/mooreryan/ZetaHunter","commit_stats":null,"previous_names":[],"tags_count":38,"template":false,"template_full_name":null,"purl":"pkg:github/mooreryan/ZetaHunter","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mooreryan%2FZetaHunter","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mooreryan%2FZetaHunter/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mooreryan%2FZetaHunter/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mooreryan%2FZetaHunter/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mooreryan","download_url":"https://codeload.github.com/mooreryan/ZetaHunter/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mooreryan%2FZetaHunter/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28618803,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-20T22:24:05.405Z","status":"ssl_error","status_checked_at":"2026-01-20T22:20:31.342Z","response_time":117,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":["classification","otus","ssu-rrna","taxonomy","zetaproteobacteria"],"created_at":"2026-01-20T23:36:31.585Z","updated_at":"2026-01-20T23:36:32.256Z","avatar_url":"https://github.com/mooreryan.png","language":"Ruby","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ZetaHunter\n\n[![Build Status](https://travis-ci.org/mooreryan/ZetaHunter.svg?branch=master)](https://travis-ci.org/mooreryan/ZetaHunter)\n\n## Citation\n\nIf you find ZetaHunter useful in your research, please cite the [ZetaHunter manuscript](http://dx.doi.org/10.1128/MRA.00932-18).\n\n```\nMcAllister, S. M., Moore, R. M., and Chan, C. S. ZetaHunter, a Reproducible Taxonomic Classification Tool for Tracking the Ecology of the Zetaproteobacteria and Other Poorly Resolved Taxa. Aug 2018, 7 (7) e00932-18; DOI: 10.1128/MRA.00932-18.\n```\n\nOr you can download the citation and import it into your favorite reference manager!\n\n- [BibTeX](https://raw.githubusercontent.com/mooreryan/ZetaHunter/master/citation/zeta_hunter.bib)\n- [EndNote](https://raw.githubusercontent.com/mooreryan/ZetaHunter/master/citation/zeta_hunter.enw)\n- [RIS](https://raw.githubusercontent.com/mooreryan/ZetaHunter/master/citation/zeta_hunter.ris)\n\n## Wiki\n\nCheck the [ZetaHunter Wiki](https://github.com/mooreryan/ZetaHunter/wiki) for\nmore info!  There you will find help on how to install and run ZetaHunter, as well as a lot more details about how ZetaHunter works.\n\n## Example datasets\n\nCheck out [ZetaHunter example datasets](https://github.com/mooreryan/ZetaHunter_examples) if you would like to check out some sample data and output from ZetaHunter.  There, you will also find a step by step guide to generating the expected output. You can also find the same sample input and curated database files [here](https://github.com/mooreryan/ZetaHunter/tree/master/example_data).\n\n## Overview\n\nZetaHunter is a command line script designed to assign user-supplied\nsmall subunit ribosomal RNA (SSU rRNA) gene sequences to OTUs defined\nby a reference sequence database.\n\nBy default, ZetaHunter uses a curated database of full-length,\nnon-chimeric, Zetaproteobacteria SSU rRNA gene sequences derived from\narb SILVA (release 128) and Zetaproteobacteria genomes from JGI's\nIntegrated Microbial Genomes (IMG). OTU definitions are the same as\nthose suggested by McAllister et al. (2011) at 97% identity, with\nnovel OTUs discovered since that publication named ZetaOTU29 and\nhigher (curated OTUs only). Infiles aligned by the arb SILVA SINA web\naligner are masked using the same 1282 bp mask used in McAllister et\nal. (2011) to obtain reproducible OTU calls through closed reference\nOTU binning. User sequences that represent novel Zetaproteobacteria\nOTUs are de novo binned into NewZetaOTUs, numbered by abundance.\n\nOTU network analysis is a simple way to visualize the connectivity of\nOTUs within a sample or environment type. ZetaHunter will output edge\nand node tab-delimited files for import into cytoscape. The node file\ncontains the abundance information for each node. The edge file lists\nOTUs that are found within the same sample (node1, node2, sample), thus\nallowing for visualization. Note: Samples with only one ZetaOTU will contain\na self referential edge. Otherwise, only non-self connections are shown.\n\nZetaHunter also supports user-provided curated OTU databases for\nsequence OTU binning of any SINA-aligned SSU rRNA sequences.\n\n## Features\n\n1. Stable SSU rRNA gene OTU binning to a curated database\n2. Supports import of multiple files for easy comparison of NewZetaOTUs across samples\n3. Database and sequence mask management options\n4. Multi-threaded processing\n5. Chimera checking\n6. Flags for sequences not related to the curated database (i.e. not Zetaproteobacteria)\n7. Cytoscape-compatible output file for OTU network analysis\n\n## Help\n\nIf you run into problems or need help with using ZetaHunter, please email us at: [zetahunter.help@gmail.com](mailto:zetahunter.help@gmail.com)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmooreryan%2Fzetahunter","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmooreryan%2Fzetahunter","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmooreryan%2Fzetahunter/lists"}