{"id":18448831,"url":"https://github.com/sequana/multicov","last_synced_at":"2025-04-08T01:32:40.105Z","repository":{"id":115174809,"uuid":"225597033","full_name":"sequana/multicov","owner":"sequana","description":"Snakemake pipeline wrapping sequana_coverage to analyse several samples at the same time","archived":false,"fork":false,"pushed_at":"2023-05-23T21:27:33.000Z","size":10311,"stargazers_count":2,"open_issues_count":1,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-03-23T03:51:16.245Z","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}},"created_at":"2019-12-03T10:52:04.000Z","updated_at":"2023-03-03T01:49:25.000Z","dependencies_parsed_at":null,"dependency_job_id":"377d703b-19b8-4a6a-a24f-fc5ee00cbe10","html_url":"https://github.com/sequana/multicov","commit_stats":null,"previous_names":["sequana/coverage"],"tags_count":4,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fmulticov","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fmulticov/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fmulticov/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Fmulticov/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sequana","download_url":"https://codeload.github.com/sequana/multicov/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247760629,"owners_count":20991518,"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":"2024-11-06T07:17:25.012Z","updated_at":"2025-04-08T01:32:39.462Z","avatar_url":"https://github.com/sequana.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"This is is the **coverage** pipeline from the `Sequana \u003chttps://sequana.readthedocs.org\u003e`_ project\n\n\n.. image:: https://badge.fury.io/py/sequana-multicov.svg\n     :target: https://pypi.python.org/pypi/sequana_multicov\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/multicov/actions/workflows/main.yml/badge.svg\n   :target: https://github.com/sequana/multicov/actions/workflows    \n\n\n:Overview: Parallelised version of sequana_coverage for large eukaryotes genome.\n:Input: A set of BAM or BED files. BED file must have 3 or 4 columns. First column is\n    the chromosome/contig name, second column stored positions and third the\n    coverage. Fourth optional columns contains a filtered coverage (not used in\n    the analysis but shown in the HTML reports)\n:Output: a set of HTML reports for each chromosomes and a multiqc report\n:Status: production\n:Citation: \n    Dimitri Desvillechabrol, Christiane Bouchier, Sean Kennedy, Thomas Cokelaer\n    *Sequana coverage: detection and characterization of genomic variations \n    using running median and mixture models*\n    GigaScience, Volume 7, Issue 12, December 2018, giy110, \n    https://doi.org/10.1093/gigascience/giy110\n\n    and \n\n    Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI https://doi:10.21105/joss.00352\n\n\nInstallation\n~~~~~~~~~~~~\n\n\nsequana_multicov is based on Python3, just install the package as follows::\n\n    pip install sequana_multicov --upgrade\n\n\nUsage\n~~~~~\n\n::\n\n    sequana_multicov --help\n    sequana_multicov --input-directory DATAPATH \n\nBy default, this looks for BED file. WARNING. This are BED3 meaning a 3-columns\ntabulated file like this one::\n\n    chr1 1 10\n    chr1 2 11\n    ...\n    chr1 N1 10\n    chr2 1 20\n    chr2 2 21\n    ...\n    chr2 N2 20\n\nwhere the first column stored the chromosome name, the second is the position\nand the third is the coverage itself. See sequana_coverage documentation for\ndetails. If you have BAM files as input, we will do the conversion for you. In\nsuch case, use this option::\n\n    --input-pattern \"*.bam\"\n\nThe sequana_coverage script creates a directory with the pipeline and \nits configuration file. You will then need \nto execute the pipeline::\n\n    cd coverage\n    sh coverage.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 multicov.rules -c config.yaml --cores 4 --stats stats.txt\n\nOr use `sequanix \u003chttps://sequana.readthedocs.io/en/master/sequanix.html\u003e`_ interface as follows::\n\n    sequanix -w analysis -i . -p coverage\n\nGo to the second panel, in Input data and then in Input directory. There, you\nmust modify the pattern (empty field by default meaning search for fastq files)\nand set the field to either::\n\n    *.bed\n\nor::\n\n    *.bam\n\n\nYou are ready to go. Save the project and press Run. Once done, open the HTML report.\n\n\nRequirements\n~~~~~~~~~~~~\n\nThis pipelines requires the following executable(s):\n\n- sequana_coverage from **Sequana**, which should be installed automatically.\n- multiqc\n\n.. .. image:: https://raw.githubusercontent.com/sequana/multicov/master/sequana_pipelines/multicov/dag.png\n\n\nDetails\n~~~~~~~~~\n\nThis pipeline runs **coverage** in parallel on the input BAM files (or BED file). \n\n\nThe coverage tool takes as input a BAM or a BED file. The BED file must have 3\nor 4 columns as explained in the standalone application (sequana_coverage) \n`documentation \u003chttp://sequana.readthedocs.io/en/master/applications.html?highlight=coverage#sequana-coverage\u003e`_. \nIn short, the first column is the chromosome name, the second column is the\nposition (sorted) and the third column is the coverage (an optional fourth\ncolumn would contain a coverage signal, which could be high quality coverage for\ninstance).\n\nIf you have only BAM files, you can convert them using **bioconvert** tool or\nthe command::\n\n    samtools depth -aa input.bam \u003e output.bed\n\nIf you have a CRAM file::\n\n    samtools view -@ 4 -T reference.fa -b -o out.bam  in.cram\n\nFor very large BAM/BED files, we recommend to split the BED file by\nchromosomes. For instance for the chromosome  chr1, type::\n\n    # samtools index in.bam\n    samtools depth -aa input.bam -r chr1 in.bam \u003e chr1.bed\n\nThe standalone or Snakemake application can also take as input your BAM file and\nwill convert it automatically into a BED file.\n\n\nRules and configuration details\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nHere is the `latest documented configuration file \u003chttps://raw.githubusercontent.com/sequana/multicov/main/sequana_pipelines/multicov/config.yaml\u003e`_\nto be used with the pipeline. Each rule used in the pipeline may have a section in the configuration file. \n\n\nChangelog\n~~~~~~~~~\n\n========= ====================================================================\nVersion   Description\n========= ====================================================================\n1.1.0     * set apptainer containers and use wrappers\n1.0.0     * renamed into multicov.\n          * update to use latest sequana_pipetools (v0.9.2)\n0.9.1     * rename genbank field into annotation, window into window_size\n0.9.0     * first version\n========= ====================================================================\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Fmulticov","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsequana%2Fmulticov","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Fmulticov/lists"}