{"id":18448857,"url":"https://github.com/sequana/lora","last_synced_at":"2026-01-22T14:45:23.786Z","repository":{"id":115174763,"uuid":"350406296","full_name":"sequana/lora","owner":"sequana","description":"Run assembler (Canu, flye, hifiasm) on a set of long read files","archived":false,"fork":false,"pushed_at":"2023-12-16T20:55:40.000Z","size":377,"stargazers_count":1,"open_issues_count":7,"forks_count":2,"subscribers_count":2,"default_branch":"main","last_synced_at":"2023-12-16T21:35:59.139Z","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}},"created_at":"2021-03-22T16:05:24.000Z","updated_at":"2023-12-20T16:03:15.241Z","dependencies_parsed_at":"2023-12-20T16:14:01.487Z","dependency_job_id":null,"html_url":"https://github.com/sequana/lora","commit_stats":null,"previous_names":[],"tags_count":0,"template":null,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Flora","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Flora/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Flora/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sequana%2Flora/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sequana","download_url":"https://codeload.github.com/sequana/lora/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":249060216,"owners_count":21206292,"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":"2024-11-06T07:17:28.445Z","updated_at":"2026-01-22T14:45:23.780Z","avatar_url":"https://github.com/sequana.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n.. image:: https://badge.fury.io/py/sequana-lora.svg\n     :target: https://pypi.python.org/pypi/sequana_lora\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/lora/actions/workflows/main.yml/badge.svg\n   :target: https://github.com/sequana/lora/actions/workflows/main.yaml\n\n\nThis is the **lora** pipeline from the `Sequana \u003chttps://sequana.readthedocs.org\u003e`_ project\n\n:Overview: Run assembler (Canu, flye, hifiasm) on a set of long read files\n:Input: A set of BAM files from Pacbio sequencers, or FastQ files for Nanopore sequencers.\n:Output: HTML reports with assemblies for each sample.\n:Status: prod\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:Citation(pipeline):\n    .. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.18337877.svg\n        :target: https://doi.org/10.5281/zenodo.18337877\n    https://www.biorxiv.org/content/10.64898/2026.01.06.697901v1\n\n.. image:: https://raw.githubusercontent.com/sequana/lora/master/sequana_pipelines/lora/dag.png\n\n\nInstallation\n~~~~~~~~~~~~\n\nInstall Lora with pip command::\n\n    pip install sequana-lora\n\nTo update your installed version, type::\n\n    pip install sequana-lora --upgrade\n\nUsage\n~~~~~\n\n::\n\n    sequana_lora --help\n    sequana_lora --input-directory DATAPATH --assembler flye\n\nThis creates a directory with the pipeline and configuration file. You will then need\nto execute the pipeline::\n\n    cd lora\n    sh lora.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 lora.rules --cores 4 --stats stats.txt\n\n\nExample 1 Pacbio - HiFi data\n----------------------------\n\nWith HiFi data, set the data-type to pacbio-hifi. We recommend flye that is quite fast with HiFi data.\nNo need to install third-party software if you use the --apptainer-prefix. It will download required files once for all.\n--do-coverage is optional but recommended to check the quality of the final contigs and their coverage.\n\n::\n\n    sequana_lora \\\n        --input-directory FILLME \\\n        --data-type pacbio-hifi \\\n        --assembler flye \\\n        --apptainer-prefix A_DIRECTORY_TO_STORE_CONTAINERS \\\n        --do-coverage  \\\n        --genome-size 35m\n\n\nExample 1 Pacbio subreads\n~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\n::\n\n    sequana_lora --input-directory . --pacbio\n    cd lora\n\n**Do you need to build CCS ?**\n\nLook at the config file and the CCS section. Check that the parameters are as expected.\nIf you wish to build so-called HiFi reads, set the min-passes to 10 and min-rq to 0.99.\n\n**do you have a blast DB**\n\nYou may also edit the config file to set blast to true (you must handle the blast databases yourself)\n\n**Do you need an annotation from your contigs?**\n\nSet prokka to True (for bacterial annotation)\n\n**Want to check the core genome?**\n\nYou may set busco to true to detect the core genome (you must provide a path to a valid lineage).\n\n\nRequirements\n~~~~~~~~~~~~\n\nThis pipelines requires the following executable(s):\n\n- canu\n- hifiasm\n- flye\n- blastn\n- busco\n- bwa\n- ccs\n- circlator\n- checkm\n- medaka\n- minimap2\n- pbindex\n- polypolish\n- prokka\n- samtools\n- sequana\n\n\n.. image:: https://raw.githubusercontent.com/sequana/lora/master/sequana_pipelines/lora/dag.png\n\n\nDetails\n~~~~~~~~~\n\nThis pipeline runs **lora** in parallel on the input fastq files (paired or not).\nA brief sequana summary report is also produced.\n\nIn practice, you may start from BAM files generated by Pacbio sequencers or\nFastq files, or CCS files. CCS files can be built by the pipeline. Then, an\nassembler is used to build the draft assemblies (Canu, hifiasm, etc). From the\ndraft, circularisation may be applied to generate circularised genome (useful\nfor bacterial genomes). Finally, each contig is blasted and quality checks are\nperformed using Busco, quast, etc.\n\n\nRules and configuration details\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n\nHere is the `latest documented configuration file \u003chttps://raw.githubusercontent.com/sequana/sequana_lora/master/sequana_pipelines/lora/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========= ====================================================================\n1.0.2     * dummy release for linking releases on Zenodo\n1.0.1     * Fix bs4 requirements\n1.0.0     * uniformised extension with other pipelines. fix regression on\n            schema file\n          * update sequana container to v0.16.5\n          * add unicyler apptainer\n          * add checkm module to help users chosing correct marker and name.\n          * replaces --pacbio and --nanopore with --data-type. pacbio is now\n            decompose into 3 sub-categories: pacbio-raw, pacbio-hifi and pacbio-corr\n          * add bandage if assembly graph is available\n          * fixed hifiasm container to use newest version\n          * improved report html\n          * make genome-size compulsary\n          * add fastp as preprocessing tool\n          * remove presets in favor of click options\n          * CCS defaults to hifi. pacbio presets in config set to pacbio-hifi\n          * blast removes from default. users must set blast DB themselves.\n          * busco lineage downloaded from the web.\n          * CANU preset changes: pacbio--\u003epacbio-hifi\n          * CANU-correction preset changes: pacbio--\u003epacbio-hifi\n          * FLYE preset changes: pacbio-raw--\u003epacbio-hifi\n0.3.0     * Use click instead of argparse\n          * added multiqc / checkm / unicycler\n0.2.0     * add apptainers in most rules\n          * remove utils.smk to move rulegraph inside main pipeline\n          * rename lora.smk into lora.rules for consistency with other\n            pipelines\n          * add checkm in the pipeline and HTML report\n0.1.0     **First release.**\n========= ====================================================================\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Flora","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsequana%2Flora","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsequana%2Flora/lists"}