{"id":41034971,"url":"https://github.com/maxibor/kraken-nf","last_synced_at":"2026-01-22T10:31:53.361Z","repository":{"id":50153468,"uuid":"196201476","full_name":"maxibor/kraken-nf","owner":"maxibor","description":"Simple Kraken2 Nextflow pipeline","archived":false,"fork":false,"pushed_at":"2021-12-02T15:55:29.000Z","size":31337,"stargazers_count":5,"open_issues_count":2,"forks_count":3,"subscribers_count":0,"default_branch":"master","last_synced_at":"2025-12-17T09:42:43.923Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/maxibor.png","metadata":{"files":{"readme":"README.md","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}},"created_at":"2019-07-10T12:29:54.000Z","updated_at":"2024-08-02T16:06:53.000Z","dependencies_parsed_at":"2022-09-16T04:41:06.865Z","dependency_job_id":null,"html_url":"https://github.com/maxibor/kraken-nf","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/maxibor/kraken-nf","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxibor%2Fkraken-nf","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxibor%2Fkraken-nf/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxibor%2Fkraken-nf/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxibor%2Fkraken-nf/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/maxibor","download_url":"https://codeload.github.com/maxibor/kraken-nf/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/maxibor%2Fkraken-nf/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28661874,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-22T01:17:37.254Z","status":"online","status_checked_at":"2026-01-22T02:00:07.137Z","response_time":144,"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":"2026-01-22T10:31:52.587Z","updated_at":"2026-01-22T10:31:53.352Z","avatar_url":"https://github.com/maxibor.png","language":"Nextflow","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Build Status](https://travis-ci.org/maxibor/kraken-nf.svg?branch=master)](https://travis-ci.org/maxibor/kraken-nf)\n\n# Kraken-nf\n\nSimple [Kraken2](https://github.com/DerrickWood/kraken2)/[Bracken](https://github.com/jenniferlu717/Bracken) Nextflow pipeline\n\n## Dependancies\n\n- [conda](https://conda.io/en/latest/)\n- [Nextflow](https://www.nextflow.io/) : `conda install -c bioconda nextflow`\n\n## Usage\n\n```\nnextflow run maxibor/kraken-nf --reads \"/path/to/paired_end_reads_*.{1,2}.fastq.gz\" --krakendb \"/path/to/minikraken2_v2_8GB_201904_UPDATE.tgz\"\n```\n\n### Input\n\n#### --reads\n\nUse this to specify the location of your input FastQ files. For example:\n\n`--reads 'path/to/data/sample_*_{1,2}.fastq'`\n\n**Please note the following requirements:**\n\n- The path must be enclosed in quotes\n- The path must have at least one \\* wildcard character\n- When using the pipeline with paired end data, the path must use {1,2} notation to specify read pairs.\n\n#### --krakendb\n\nPath to Kraken2 MiniKraken2_v2_8GB Database. A pre-build database can be downloaded [here](https://benlangmead.github.io/aws-indexes/k2)\n\n#### --kraken_mem\n\nAmount of memory allocated to Kraken2.\nDepends on the kraken database.\n\nExample:\n\n```bash\n--kraken_mem '9G'\n```\n\n## Kraken2 database\n\nAny Kraken2 database can be used, but the _PlusPFP-8_ is a good compromise between speed and accuracy.  \nPlease have a look at the [Index zone](https://benlangmead.github.io/aws-indexes/k2) to download it.\n\n## Help\n\n```\n$ nextflow run maxibor/kraken-nf --help\nN E X T F L O W  ~  version 21.04.0\n\n kraken-nf: simple Kraken2/Bracken Nextflow pipeline\n Homepage: https://github.com/maxibor/kraken-nf\n Author: Maxime Borry \u003cmaxime_borry@eva.mpg.de\u003e\n=========================================\nUsage:\nThe typical command for running the pipeline is as follows:\nnextflow run maxibor/kraken-nf --reads '/path/to/paired_end_reads_*.{1,2}.fastq.gz' --krakendb '/path/to/minikraken2_v2_8GB_201904_UPDATE.tgz'\nMandatory arguments:\n  --reads                       Path to input data (must be surrounded with quotes)\n  --krakendb                    Path to MiniKraken2_v2_8GB Database\n  --kraken_mem                  Memory allocated to kraken2. Ex: '4G'. Default to 9G\n\nSettings:\n  --minimum_read_length         Minimum read length to keep. Default to null\n  --minhit                      Minimum number of Kraken hits to report Taxonomic level. Defaults to 10\n  --phred                       Specifies the fastq quality encoding (33 | 64). Defaults to 33\n  --pairedEnd                   Specified if reads are paired-end (true | false). Default = true\n  --build_bracken_db            Build Bracken database (true | false). Default = false\n  --run_bracken                 Run Bracken (true | false). Default = true\n  --bracken_level               Specifies the taxonomic level for Bracken. Default = S\n  --bracken_threshold           Specifies the threshold for Bracken. Default = 10\n\nOptions:\n  --results                     The output directory where the results will be saved. Defaults to ./results\n  --help  --h                   Shows this help page\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaxibor%2Fkraken-nf","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmaxibor%2Fkraken-nf","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaxibor%2Fkraken-nf/lists"}