{"id":13710061,"url":"https://github.com/haowenz/sigmap","last_synced_at":"2025-05-06T18:33:53.624Z","repository":{"id":47251965,"uuid":"242170382","full_name":"haowenz/sigmap","owner":"haowenz","description":"A streaming method for mapping nanopore raw signals","archived":false,"fork":false,"pushed_at":"2021-11-07T15:36:34.000Z","size":608,"stargazers_count":30,"open_issues_count":4,"forks_count":6,"subscribers_count":1,"default_branch":"master","last_synced_at":"2024-08-03T23:17:18.191Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"C++","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/haowenz.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}},"created_at":"2020-02-21T15:27:34.000Z","updated_at":"2024-05-25T06:52:28.000Z","dependencies_parsed_at":"2022-07-22T05:48:13.169Z","dependency_job_id":null,"html_url":"https://github.com/haowenz/sigmap","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haowenz%2Fsigmap","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haowenz%2Fsigmap/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haowenz%2Fsigmap/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/haowenz%2Fsigmap/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/haowenz","download_url":"https://codeload.github.com/haowenz/sigmap/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224521513,"owners_count":17325250,"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":"2024-08-02T23:00:51.410Z","updated_at":"2024-11-13T20:31:00.604Z","avatar_url":"https://github.com/haowenz.png","language":"C++","funding_links":[],"categories":["Software packages"],"sub_categories":["Adaptive sampling / ReadUntil Real-time mapping / signal mapping"],"readme":"# Sigmap\nSigmap is a streaming method for mapping raw nanopore signal to reference genomes.\n\n## Installation\nFirst get the repo with submodules (make sure you use `--recursive`):\n```\ngit clone --recursive git@github.com:haowenz/sigmap.git\n```\nMake sure you have GCC version \u003e 8. Then just run:\n```\ncd sigmap \u0026\u0026 make\n```\n\n## Usage\nFirst, an index needs to be built for the reference using ONT pore models (as a submodule in the extern folder). We use yeast genome as an example:\n```\n./sigmap -i -r yeast.fasta -p extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model -o yeast_index\n```\nIt will generate the index file *yeast_index.si*. Note that a genome point cloud file *yeast_index.pt* will also be saved. But it can also be generated very quickly on the fly every time before mapping. After index construction, yeast raw signals in fast5 format or blow5 format can be mapped using\n```\n./sigmap -m -r yeast.fasta -p extern/kmer_models/r9.4_180mv_450bps_6mer/template_median68pA.model -x yeast_index -s /path/to/yeast/fast5_or_blow5/dir -o yeast_mapping.paf -t 4\n```\nThis command map all the fast5 and blow5 reads in `/path/to/yeast/fast5_or_blow5/dir` and its subdirectories to the yeast genome using 4 threads. The output will be saved to `yeast_mapping.paf` in a modified PAF format used by [Uncalled](https://github.com/skovaka/UNCALLED).\n\nMany other parameters can be found in the help information:\n```\n./sigmap -h\n```\n\nIt is possible that your reads in fast5 files are compressed with the [VBZ compression](https://github.com/nanoporetech/vbz_compression) from Nanopore. Then you have to download the proper HDF5 plugin from [here](https://github.com/nanoporetech/vbz_compression/releases) and make sure it can be found by your HDF5 library:\n```\nexport HDF5_PLUGIN_PATH=/path/to/hdf5/plugins/lib\n```\n\n## Getting help\nIf you encounter bugs or have further questions or requests, you can raise an issue at the [issue page](https://github.com/haowenz/sigmap/issues) or contact me by email hwzhang@gatech.edu.\n\n## Citing Sigmap\nIf you use Sigmap, please cite:\n\nZhang, H., Li, H., Jain, C., Cheng, H., Au, K. F., Li, H., \u0026 Aluru, S. (2021). Real-time mapping of nanopore raw signals. Bioinformatics, 37(Supplement_1), i477-i483. https://doi.org/10.1093/bioinformatics/btab264\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhaowenz%2Fsigmap","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhaowenz%2Fsigmap","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhaowenz%2Fsigmap/lists"}