{"id":19492021,"url":"https://github.com/meeranhussain/population_genomic_analysis","last_synced_at":"2026-06-19T10:32:14.037Z","repository":{"id":244630540,"uuid":"815773855","full_name":"meeranhussain/Population_genomic_analysis","owner":"meeranhussain","description":"A repository for efficient population genomic analysis using Snakemake workflow.","archived":false,"fork":false,"pushed_at":"2025-04-21T05:33:56.000Z","size":941,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-04-21T06:38:46.872Z","etag":null,"topics":["genome-analysis","ngs","ngs-analysis","population","population-genomics","rprogramming","snakemake-workflow","variant-calling","whole"],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/meeranhussain.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"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}},"created_at":"2024-06-16T05:34:11.000Z","updated_at":"2025-04-21T05:33:59.000Z","dependencies_parsed_at":"2024-11-10T21:19:26.321Z","dependency_job_id":"bc520fbb-1642-4dc7-93cb-a7c752e36885","html_url":"https://github.com/meeranhussain/Population_genomic_analysis","commit_stats":null,"previous_names":["meeranhussain/population_genomic_analysis"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/meeranhussain/Population_genomic_analysis","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/meeranhussain%2FPopulation_genomic_analysis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/meeranhussain%2FPopulation_genomic_analysis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/meeranhussain%2FPopulation_genomic_analysis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/meeranhussain%2FPopulation_genomic_analysis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/meeranhussain","download_url":"https://codeload.github.com/meeranhussain/Population_genomic_analysis/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/meeranhussain%2FPopulation_genomic_analysis/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34528134,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-19T02:00:06.005Z","response_time":61,"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":["genome-analysis","ngs","ngs-analysis","population","population-genomics","rprogramming","snakemake-workflow","variant-calling","whole"],"created_at":"2024-11-10T21:19:06.895Z","updated_at":"2026-06-19T10:32:14.017Z","avatar_url":"https://github.com/meeranhussain.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Unlocking Genomic Insights: Efficient Population Analysis using Snakemake\n\nThis GitHub repository includes steps to run snakemake file that help in performing population genomics analysis using whole genome resequencing data. Here, you'll find Snakemake file designed to parallelize the steps involved in these analyses, making the workflow more efficient and speeding up the process.\n\n**Current Workflow:**\nThe current workflow covers the entire process from short read data processing to the establishment of population structure i.e. PCA (Principal Component Analysis) plotting. This setup uses Snakemake workflow language to streamline and automate these tasks.\n\n**Future Updates:**\nStay tuned for future updates, which will include additional analyses such as Fst analysis, admixture analysis, and more.\nFeel free to explore the repositories, and don't hesitate to reach out if you have any questions or suggestions!\n\nThis snakmake workflow was created using commands from [Elahe Parvizi's](https://github.com/Elahep) GitHub repositories. \n\n![image](https://github.com/meeranhussain/Population_genomics_analysis/assets/40800675/26de3f9c-b8c4-4b46-95a1-fd495d22d0cf)\n\n\n# FOR SNAKEMAKE RUN\n## Step 1: Project Folder\nCreate a project folder and give it a meaningful Project_ID.\n```bash\nmkdir \u003cproject-id\u003e\n```\n## Step 2: Copy Files into Project Folder\nCopy the following files into the project folder:\n- `Snakefile`\n- `Stats.R`\n- `config.yaml`\n\n## Step 3: Create a Sub-folder \"01_Data\"\nInside the project folder, create a sub-folder named `01_Data`.\n```bash\nmkdir \u003cproject-id\u003e/01_Data\n```\n## Step 4: Copy Sample Files to 01_Data\nCopy the sample files into the `01_Data` folder. \n```bash\ncp *.fq \u003cproject-id\u003e/01_Data\n```\nEnsure that the fastq files are named according to this pattern. **Ex: Featherston_01.fastq, Featherston_02.fastq, Mosburn_01.fastq**\n#### Explanation of Example\nTo help you understand how to label the files correctly:\n- `Each file should have a name followed by an underscore and a two-digit number.`\n- `The name represents a specific population or sample, such as \"Featherston\" or \"Mosburn\".`\n- `The two-digit number distinguishes different files from the same population or sample.`\n\n## Step 5: Use Config File to Add Additional Information\nUtilize the `config.yaml` file to add any additional information required for the workflow.\n#### config.yaml content for snakemake workflow (Example file)\n\n```yaml\n##### Sequencing platform info (mostly keep this constant)\nPL: \"Illumina\"\nPM: \"HISEQ\"\n\n##### Assign threads \nTHREADS: 16\n\n##### Provide path to reference file (Ensure reference is indexed using BWA index command and available in path provided)\nfasta_path: /path/to/.fasta\n\n######## Variant calling filter parameters ########\nmin_MQ: 20\nmin_BQ: 20\nvcf_name: 'M_aethio_MOSS_LIN_FEA' #Used to assign names to output files generated in most steps\nMAF: 'MAF \u003e 0.05'\n\n######## PLINK parameters #################\nGENO: 0.1\n```\n\n## Step 6: Run Snakemake\nNavigate to the project folder in your terminal.\n\n**Perform dry-run to test the script using \"-n\" flag:**\n```bash\nsnakemake --configfile=config.yaml --cores 8 -n\n```\n**Proper execution use the following:**\n```bash\nsnakemake --configfile=config.yaml --cores 8 \n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmeeranhussain%2Fpopulation_genomic_analysis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmeeranhussain%2Fpopulation_genomic_analysis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmeeranhussain%2Fpopulation_genomic_analysis/lists"}