{"id":18448854,"url":"https://github.com/sequana/depletion","last_synced_at":"2025-08-25T00:35:27.757Z","repository":{"id":115174661,"uuid":"475947632","full_name":"sequana/depletion","owner":"sequana","description":"Deplete Fastq files from human or other content","archived":false,"fork":false,"pushed_at":"2024-05-22T08:13:22.000Z","size":15996,"stargazers_count":1,"open_issues_count":2,"forks_count":2,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-07-19T12:21:41.750Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sequana.png","metadata":{"files":{"readme":"README.rst","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}},"created_at":"2022-03-30T15:46:37.000Z","updated_at":"2023-01-31T10:47:45.000Z","dependencies_parsed_at":"2024-06-12T16:50:37.584Z","dependency_job_id":null,"html_url":"https://github.com/sequana/depletion","commit_stats":{"total_commits":9,"total_committers":1,"mean_commits":9.0,"dds":0.0,"last_synced_commit":"9cbf5adab6c43ed15b200d0ea51c8a5a8fb94fc9"},"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/sequana/depletion","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fdepletion","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fdepletion/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fdepletion/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fdepletion/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sequana","download_url":"https://codeload.github.com/sequana/depletion/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fdepletion/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":271984416,"owners_count":24853820,"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","status":"online","status_checked_at":"2025-08-24T02:00:11.135Z","response_time":111,"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":[],"created_at":"2024-11-06T07:17:27.980Z","updated_at":"2025-08-25T00:35:27.677Z","avatar_url":"https://github.com/sequana.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n.. image:: https://badge.fury.io/py/sequana-depletion.svg\n     :target: https://pypi.python.org/pypi/sequana_depletion\n\n.. image:: http://joss.theoj.org/papers/10.21105/joss.00352/status.svg\n    :target: http://joss.theoj.org/papers/10.21105/joss.00352\n    :alt: JOSS (journal of open source software) DOI\n\n.. image:: https://github.com/sequana/depletion/actions/workflows/main.yml/badge.svg\n   :target: https://github.com/sequana/depletion/actions/workflows    \n\n\n\n\nThis is is the **depletion** pipeline from the `Sequana \u003chttps://sequana.readthedocs.org\u003e`_ project\n\n:Overview: select or deplete reads from input FastQ files given a reference\n:Input: Fastq Files\n:Output: Fastq Files\n:Status: production\n:Citation: Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352\n\n\nInstallation\n~~~~~~~~~~~~\n\nInstall this package as follows::\n\n    pip install sequana_depletion\n\nit requires https://sequana.readthedocs.io and https://bioconvert.readthedocs.io for the bam to fastq conversion\n\n\nUsage\n~~~~~\n\n::\n\n    sequana_depletion --help\n    sequana_depletion --input-directory DATAPATH --reference hg38.fa --mode depletion\n    sequana_depletion --input-directory DATAPATH --reference covid.fa --mode selection\n\nThis creates a directory with the pipeline and configuration file. You will then need\nto execute the pipeline::\n\n    cd depletion\n    sh depletion.sh  # for a local run\n\nThis launch a snakemake pipeline. If you are familiar with snakemake, you can\nretrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters::\n\n    snakemake -s depletion.rules -c config.yaml --cores 4 --stats stats.txt\n\nOr use `sequanix \u003chttps://sequana.readthedocs.io/en/master/sequanix.html\u003e`_ interface.\n\nRequirements\n~~~~~~~~~~~~\n\nThis pipelines requires the following executable(s):\n\n- bwa\n- samtools\n- bamtools\n\n#.. image:: https://raw.githubusercontent.com/sequana/depletion/master/sequana_pipelines/depletion/dag.png\n\n\nDetails\n~~~~~~~~~\n\nThis pipeline runs **depletion** in parallel on the input fastq files (paired or not). \nA brief sequana summary report is also produced.\n\n\nRules and configuration details\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nHere is the `latest documented configuration file \u003chttps://raw.githubusercontent.com/sequana/depletion/master/sequana_pipelines/depletion/config.yaml\u003e`_\nto be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file. \n\nChangelog\n~~~~~~~~~\n\n========= ====================================================================\nVersion   Description\n========= ====================================================================\n0.3.0     * use click and new sequana_pipetools. convert to pyproject\n0.2.0     * handle paired/unpaired data\n          * refactorise to use containers/apptainers\n0.1.0     **First release.**\n========= ====================================================================\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Fdepletion","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsequana%2Fdepletion","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Fdepletion/lists"}