{"id":29224598,"url":"https://github.com/sing-group/metatax","last_synced_at":"2026-02-01T21:38:00.764Z","repository":{"id":88302769,"uuid":"348306501","full_name":"sing-group/metatax","owner":"sing-group","description":"Metatax: Metataxonomics with a Compi-based pipeline for Precision Medicine","archived":false,"fork":false,"pushed_at":"2021-03-17T08:46:33.000Z","size":13,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":5,"default_branch":"master","last_synced_at":"2026-01-15T05:04:20.509Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Dockerfile","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/sing-group.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2021-03-16T10:35:17.000Z","updated_at":"2021-03-17T08:46:35.000Z","dependencies_parsed_at":null,"dependency_job_id":"d9415392-bfd2-4dfb-9418-4986f299ec0c","html_url":"https://github.com/sing-group/metatax","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/sing-group/metatax","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fmetatax","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fmetatax/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fmetatax/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fmetatax/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sing-group","download_url":"https://codeload.github.com/sing-group/metatax/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sing-group%2Fmetatax/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28991772,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-01T20:57:35.821Z","status":"ssl_error","status_checked_at":"2026-02-01T20:57:29.580Z","response_time":56,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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":"2025-07-03T06:07:25.132Z","updated_at":"2026-02-01T21:38:00.759Z","avatar_url":"https://github.com/sing-group.png","language":"Dockerfile","funding_links":[],"categories":[],"sub_categories":[],"readme":" # Metatax: Metataxonomics with a Compi-based pipeline for Precision Medicine.\r\n\r\nOsvaldo Graña-Castro, Hugo López-Fernández, Alba Nogueira-Rodríguez, Florentino Fdez-Riverola, Fátima Al-Sharour and Daniel Glez-Peña.\r\n\r\nA Docker image is available for this pipeline in [this Docker Hub repository](https://hub.docker.com/r/singgroup/metatax).\r\n\r\n\r\n\r\n\r\n\r\n\r\n# Running the pipeline with sample data\r\n\r\nIt is possible to test the pipeline using our sample data available [here](). Download the ZIP file and decompress it in your local file system. Then, run the following command, changing the `/path/to/metataxonomics/data/` to the path where you have the decompressed data.\r\n\r\n\r\n(i) Download sequencing data from SRA: \r\n\r\nRead files can be downloaded from SRA (ID SRP116709) with the following command line (provided that Docker-CE is already installed):\r\n\r\n*** Download first the required files SRR_Acc_List.txt, SraRunTable.txt, parameters.txt, map.tsv and uc_fast_params.txt from the following link: http://static.sing-group.org/software/compi/pipelines/metatax/supplementary-data-2019.08.08.zip\r\n\r\n```\r\nmkdir -p ./FASTQ \r\nfor SRR in $(cat SRR_Acc_List.txt) ; do echo $SRR; docker run -v ./FASTQ:/FASTQ --rm pegi3s/sratoolkit fastq-dump --origfmt --split-files --A $SRR -O ./FASTQ/ ; done\r\n```\r\n\r\n(ii) Data preprocessing:\r\n\r\nAs all the sequenced data in this dataset has been downloaded in step (i), we now select the samples we are working with (16S rRNA human sequences):\r\n```\r\nhead -n 1 SraRunTable.txt \u003e 16SrRNA_human.txt ; grep '^AMPLICON' SraRunTable.txt | grep 'Homo sapiens' \u003e\u003e 16SrRNA_human.txt\r\n```\r\n\r\nThen we collect the corresponding SRR* and patient codes for the selected samples to a separated file:\r\n```\r\ncut --output-delimiter=',' -f 15,20 16SrRNA_human.txt | grep -v 'Run' \u003e listOfSelectedSamples.txt\r\n```\r\n\r\nIn order to rename the samples in a clearer way, we rename them using the associated patient codes:\r\n```\r\nmkdir -p ./selectedFASTQ\r\nfor file in $(cat listOfSelectedSamples.txt); do echo $file; input=${file/,*/}; output=${file/*,/}; echo $input; echo $output; input1='./FASTQ/'${input}'_1.fastq'; input2='./FASTQ/'${input}'_2.fastq'; output1='./selectedFASTQ/'${output}'_1.fastq'; output2='./selectedFASTQ/'${output}'_2.fastq'; cp $input1 $output1; cp $input2 $output2; done\r\n```\r\n\r\n(iii) Executing metatax:\r\n\r\nCopy parameters.txt, map.tsv and uc_fast_params.txt files to ./selectedFASTQ directory\r\n\r\n\r\nDefine a metatax execution variable:\r\n```\r\nmetatax=\"docker run --rm -e DISPLAY=\"$(docker network inspect bridge --format='{{(index .IPAM.Config 0).Gateway}}'):0\" -v ./selectedFASTQ:/data -v /tmp/COMPI_logs:/tmp -i compi/metatax\"\r\n\r\n```\r\n\r\nComplete execution (all tasks):\r\n```\r\n$metatax --logs /tmp/ -pa /data/parameters.txt\r\n```\r\n\r\nAlternatively, single tasks can be excuted individually or even repeated as follows:\r\n```\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task initialization\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task validate_mapping\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task join_pe\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task multiple_splitLibFastq\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task pick_otus\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task otu_table_summary\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task otu_table_single_rarefaction\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task otu_table_alpha_rarefaction\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task core_diversity\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task alpha_divers\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task beta_divers_through_plots\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task compare_alpha_divers\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task compare_categories\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task filter_otus\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task group_sig\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task align_sequences\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task phylogeny\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task univariate_DESeq2\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task univariate_edgeR\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task ancom\r\n$metatax --logs /tmp/ -pa /data/parameters.txt --single-task selbal\r\n```\r\n\r\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsing-group%2Fmetatax","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsing-group%2Fmetatax","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsing-group%2Fmetatax/lists"}