{"id":16849270,"url":"https://github.com/mbhall88/nanovarbench","last_synced_at":"2026-03-03T20:31:09.529Z","repository":{"id":227837730,"uuid":"733285822","full_name":"mbhall88/NanoVarBench","owner":"mbhall88","description":"Evaluating Nanopore-based bacterial variant calling","archived":false,"fork":false,"pushed_at":"2025-07-23T00:20:46.000Z","size":41039,"stargazers_count":21,"open_issues_count":0,"forks_count":1,"subscribers_count":4,"default_branch":"main","last_synced_at":"2026-01-20T05:12:07.970Z","etag":null,"topics":["bacteria","benchmark","bioinformatics","illumina","microbial-genomics","nanopore","variant-calling"],"latest_commit_sha":null,"homepage":"https://doi.org/10.1101/2024.03.15.585313","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/mbhall88.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2023-12-19T01:41:31.000Z","updated_at":"2025-12-02T17:10:11.000Z","dependencies_parsed_at":"2025-04-11T06:41:21.267Z","dependency_job_id":"941bf313-5dc9-4d3c-a7e9-7ffe321ed032","html_url":"https://github.com/mbhall88/NanoVarBench","commit_stats":null,"previous_names":["mbhall88/nanovarbench"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/mbhall88/NanoVarBench","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mbhall88%2FNanoVarBench","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mbhall88%2FNanoVarBench/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mbhall88%2FNanoVarBench/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mbhall88%2FNanoVarBench/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mbhall88","download_url":"https://codeload.github.com/mbhall88/NanoVarBench/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mbhall88%2FNanoVarBench/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30058263,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-03T18:21:05.932Z","status":"ssl_error","status_checked_at":"2026-03-03T18:20:59.341Z","response_time":61,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 state=error: 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":["bacteria","benchmark","bioinformatics","illumina","microbial-genomics","nanopore","variant-calling"],"created_at":"2024-10-13T13:14:46.490Z","updated_at":"2026-03-03T20:31:09.503Z","avatar_url":"https://github.com/mbhall88.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# NanoVarBench\n\n## Evaluating Nanopore-based bacterial variant calling\n\nThis repository holds the code for [our paper][doi] which performs comprehensive benchmarking of SNP and indel variant calling accuracy across 14 diverse bacterial species using Oxford Nanopore Technologies (ONT) and Illumina sequencing.\n\nYou can find the results in that paper. Future updates after publication based on new tools, versions, experiments etc. will be reported and shown here.\n\n- [Citation](#citation)\n- [Data](#data)\n- [Usage](#usage)\n\n## Citation\n\n\u003e  Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data\nMichael B. Hall, Ryan R. Wick, Louise M. Judd, An N. T. Nguyen, Eike J. Steinig, Ouli Xie, Mark R. Davies, Torsten Seemann, Timothy P. Stinear, Lachlan J. M. Coin\n_eLife_ (2024) 13:RP98300; doi: [10.7554/eLife.98300][doi]\n\n```bibtex\n@article{hall_benchmarking_2024,\n\ttitle = {Benchmarking reveals superiority of deep learning variant callers on bacterial nanopore sequence data},\n\tvolume = {13},\n\tcopyright = {Creative Commons Attribution-ShareAlike 4.0 International License (CC-BY-SA)},\n\tissn = {2050-084X},\n\turl = {https://doi.org/10.7554/eLife.98300},\n\tdoi = {10.7554/eLife.98300},\n\turldate = {2024-10-17},\n\tjournal = {eLife},\n\tauthor = {Hall, Michael B and Wick, Ryan R and Judd, Louise M and Nguyen, An N and Steinig, Eike J and Xie, Ouli and Davies, Mark and Seemann, Torsten and Stinear, Timothy P and Coin, Lachlan},\n\teditor = {Weigel, Detlef},\n\tmonth = oct,\n\tyear = {2024},\n\tpages = {RP98300},\n}\n```\n\n## Data\n\nAccessions and DOIs for all data can be found in [`config/accessions.csv`](./config/accessions.csv).\n\nThe variant truthsets and associated data for making these is [archived on Zenodo][truth].\n\n## Usage\n\nSee [the config docs](./config/README.md) for instructions on how to configure this pipeline for your data.\n\nYou will need the following packages to run the pipeline:\n\n- `snakemake`\n- `pandas`\n- `apptainer` or `singularity`\n- `conda`\n\nA script for submitting the master Snakemake job on a Slurm cluster can be found at [`scripts/submit_slurm.sh`](./scripts/submit_slurm.sh).\n\n\n[doi]: https://doi.org/10.7554/eLife.98300 \n[truth]: https://zenodo.org/doi/10.5281/zenodo.10867170\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmbhall88%2Fnanovarbench","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmbhall88%2Fnanovarbench","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmbhall88%2Fnanovarbench/lists"}