{"id":18448825,"url":"https://github.com/sequana/laa","last_synced_at":"2025-04-15T11:27:05.297Z","repository":{"id":115174722,"uuid":"447938685","full_name":"sequana/laa","owner":"sequana","description":"Pacbio amplicon, sequana, phylogeny, variant","archived":false,"fork":false,"pushed_at":"2023-12-19T11:32:50.000Z","size":9326,"stargazers_count":1,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-01-25T12:16:30.713Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","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":"2022-01-14T11:08:14.000Z","updated_at":"2023-03-03T01:49:57.000Z","dependencies_parsed_at":null,"dependency_job_id":"0f1dcf3b-6c1a-405d-93b4-9e9014943bee","html_url":"https://github.com/sequana/laa","commit_stats":{"total_commits":13,"total_committers":1,"mean_commits":13.0,"dds":0.0,"last_synced_commit":"35c5cec15469ff77a4d6943ce8868b6b5439e9b4"},"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Flaa","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Flaa/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Flaa/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Flaa/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sequana","download_url":"https://codeload.github.com/sequana/laa/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":239132704,"owners_count":19587107,"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":"2024-11-06T07:17:24.446Z","updated_at":"2025-02-16T13:23:01.040Z","avatar_url":"https://github.com/sequana.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n.. image:: https://badge.fury.io/py/sequana-laa.svg\n     :target: https://pypi.python.org/pypi/sequana_laa\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/laa/actions/workflows/main.yml/badge.svg\n   :target: https://github.com/sequana/laa/actions/workflows/main.yml)\n\n\n\nThis is is the **laa** pipeline from the `Sequana \u003chttps://sequana.readthedocs.org\u003e`_ project\n\n:Overview: Perform amplicon analysis on Pacbio data sets including variant and phylogeny\n:Input: A set of CCS files from pacbio in FastQ formats\n:Output: variant calling, phylogney, consensus genomes, etc\n:Status: production but may change\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\nThis pipeline was used in :\n\n- L'Honneur et al (polyomavirus, 2022) https://pubmed.ncbi.nlm.nih.gov/34979561/ \n- Kali et al (rabies,2021), https://pubmed.ncbi.nlm.nih.gov/33444703/\n- Claireaux et al. (gene involved in HIV, 2022) accepted, not yet on pubmed\n\nInstallation\n~~~~~~~~~~~~\n\nYou must install Sequana first::\n\n    pip install sequana\n\nThen, just install this package::\n\n    pip install sequana_laa\n\n\nUsage\n~~~~~\n\n::\n\n    sequana_laa --help\n    sequana_laa --input-directory DATAPATH \n\nThis creates a directory with the pipeline and configuration file. You will then need \nto execute the pipeline::\n\n    cd laa\n    sh laa.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 laa.rules -c config.yaml --cores 4 --stats stats.txt --wrapper-prefix git+file:///home/cokelaer/Work/github/forked/sequana-wrappers\n\nOr use `sequanix \u003chttps://sequana.readthedocs.io/en/main/sequanix.html\u003e`_ interface.\n\nRequirements\n~~~~~~~~~~~~\n\nThis pipelines requires the following executable(s):\n\n- vt\n- freebayes\n- igvtools\n- sequana\n- snpeff (optional)\n- samtools\n- bamtools\n- minimap2\n\n.. image:: https://raw.githubusercontent.com/sequana/laa/main/sequana_pipelines/laa/dag.png\n\n\nDetails\n~~~~~~~~~\n\nThis pipeline runs amplicon analysis on long reads data from pacbio sequencers. \n\n\nRules and configuration details\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nHere is the `latest documented configuration file \u003chttps://raw.githubusercontent.com/sequana/laa/main/sequana_pipelines/laa/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========= ====================================================================\n0.10.0    full integration with latest wrapeprs and apptainers from damona\n0.9.0     add singularity containers\n0.8.0     **First release.**\n========= ====================================================================\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Flaa","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsequana%2Flaa","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Flaa/lists"}