{"id":40170837,"url":"https://github.com/lu-vedder/maizesnp","last_synced_at":"2026-01-19T17:05:32.820Z","repository":{"id":223488723,"uuid":"748584300","full_name":"lu-vedder/MaizeSNP","owner":"lu-vedder","description":"SNP analysis of different maize (Zea mays L.) inbred lines in comparison to B73 as a reference line","archived":false,"fork":false,"pushed_at":"2024-02-20T13:41:10.000Z","size":39,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-09-05T02:57:35.541Z","etag":null,"topics":["bioinformatics","genetics","maize","snp-analysis"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":false,"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/lu-vedder.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","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":"2024-01-26T10:03:37.000Z","updated_at":"2024-02-20T13:27:06.000Z","dependencies_parsed_at":"2024-02-20T14:47:01.930Z","dependency_job_id":"85ee320d-811d-4984-b55b-4c3a00477356","html_url":"https://github.com/lu-vedder/MaizeSNP","commit_stats":null,"previous_names":["lu-vedder/maizesnp"],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/lu-vedder/MaizeSNP","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lu-vedder%2FMaizeSNP","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lu-vedder%2FMaizeSNP/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lu-vedder%2FMaizeSNP/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lu-vedder%2FMaizeSNP/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lu-vedder","download_url":"https://codeload.github.com/lu-vedder/MaizeSNP/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lu-vedder%2FMaizeSNP/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28577129,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-19T16:29:19.148Z","status":"ssl_error","status_checked_at":"2026-01-19T16:29:17.772Z","response_time":67,"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":["bioinformatics","genetics","maize","snp-analysis"],"created_at":"2026-01-19T17:05:32.509Z","updated_at":"2026-01-19T17:05:32.811Z","avatar_url":"https://github.com/lu-vedder.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# MaizeSNP\n\nThe MaizeSNP wolkflow was specifically designed for the SNP analysis of different maize (_Zea mays_ L.) inbred lines in comparison to B73 as a reference line.\nThe final result is a TSV-file, containing a set of SNPs between the respective inbred line and B73, located in the protein-coding regions of maize. Further, this file includes the allele counts, obtained from the original mapping.\n\n**Workflow.txt** \u003cbr\u003e\nThe workflow file gives the exact order and parameter settings for runnig the other scripts. Please mind the following:\n* Beforehand a mapping of all merged reads of one indred line ('LINE') has been performed using Bowtie2 (performed with version v2.2.9) [1]. The resulting mapping files (SAM-files) were prepared for the SNP calling as stated in the workflow using Samtools (v1.3.1) [2] and Picard (v2.9.0) [3].\n* The SNP calling was performed using GATK (performed with version v3.7-0-gcfedb67) [4]. The input file is the before mentioned prepared mapping result.\n* The reference genome of B73 was used in version 3. The usage of new versions may need some adaptations.\n\n**filter_blacklist_merged_SNPs.py** \u003cbr\u003e\nUsing the SNPs between 'our' B73 and the reference genome as a blacklist for the filtering of \"true\" SNPs.\nThis step should reduce the mapping bias caused by variations between the reference B73 and 'our' B73 used in the lab experiments.\n\n**empty_blacklist.txt** \u003cbr\u003e\nThis is just a dummy file. It can be used as an empty blacklist file in the 'filter_blacklist_merged_SNPs.py' script.\n\n**count_SNP_alleles_mergedBAM.py - Python2 environment required!** \u003cbr\u003e\nCount the number of reads matching the Ref/SNP allele using the merged BAM files.\n\n**collect_gene_ids_from_gtf.py** \u003cbr\u003e\nCollecting the 39,469 gene IDs of the protein coding genes of Zea mays, reference version 3 (GTF-format).\n\n**collect_gene_ids_from_gff3.py** \u003cbr\u003e\nCollecting the gene IDs of the protein coding genes of Zea mays based on reference version 4 (GFF3-format).\n\n**filter_merged_snps_for_coding_genes.py** \u003cbr\u003e\nFilter the SNPs (TSV-format) for positions located in the protein-coding genes set. Allele counts may be included in the file.\n\n\n# Citation\nPlease cite via Zenodo: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10684044.svg)](https://doi.org/10.5281/zenodo.10684044) \u003cbr\u003e\nOr as: Vedder, L. (2024). MaizeSNP (Version 1.0.0) [Computer software]. https://github.com/lu-vedder/MaizeSNP (for details see the [CITATION](CITATION.cff) file).\n\n\n# License\nCopyright (c) 2024 \u003ca href=\"https://orcid.org/0000-0002-8924-9800\"\u003eLucia Vedder\u003cimg alt=\"ORCID logo\" src=\"https://info.orcid.org/wp-content/uploads/2019/11/orcid_16x16.png\" width=\"16\" height=\"16\" /\u003e\u003c/a\u003e\u003cbr\u003e\nFor details see the [LICENSE](LICENSE) file.\n\n---\n[1] https://bowtie-bio.sourceforge.net/bowtie2/index.shtml \u003cbr\u003e\n[2] http://www.htslib.org \u003cbr\u003e\n[3] https://broadinstitute.github.io/picard \u003cbr\u003e\n[4] https://gatk.broadinstitute.org\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flu-vedder%2Fmaizesnp","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flu-vedder%2Fmaizesnp","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flu-vedder%2Fmaizesnp/lists"}