{"id":20153579,"url":"https://github.com/seqan/slimm","last_synced_at":"2025-04-09T21:33:17.255Z","repository":{"id":91442803,"uuid":"51085901","full_name":"seqan/slimm","owner":"seqan","description":"Species Level Identification of Microbes from Metagenomes","archived":false,"fork":false,"pushed_at":"2019-04-30T11:37:11.000Z","size":34098,"stargazers_count":28,"open_issues_count":2,"forks_count":3,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-03-23T23:26:58.936Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C++","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/seqan.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}},"created_at":"2016-02-04T15:45:01.000Z","updated_at":"2024-12-26T10:56:01.000Z","dependencies_parsed_at":null,"dependency_job_id":"9043cd00-575f-45c8-a8d6-08629d71d591","html_url":"https://github.com/seqan/slimm","commit_stats":null,"previous_names":[],"tags_count":9,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fslimm","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fslimm/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fslimm/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/seqan%2Fslimm/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/seqan","download_url":"https://codeload.github.com/seqan/slimm/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248114981,"owners_count":21050149,"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":"2024-11-13T23:19:47.750Z","updated_at":"2025-04-09T21:33:17.225Z","avatar_url":"https://github.com/seqan.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"SLIMM - Species Level Identification of Microbes from Metagenomes\n=================================================================\n\na taxonomic profiling tool that investigates which microorganisms are present in a sequenced sample. SLIMM requires a BAM/SAM alignment file as an input. One can use a read mapper of choice to map raw reads obtained from a sequencing machine to obtain the BAM/SAM file required as input for SLIMM. \n\n\tslimm_build [OPTIONS] -nm names.dmp -nd nodes.dmp FASTA_DB nucl_gb.accession2taxid\n\tslimm [OPTIONS] $SLIMM_DB_PATH $SAM_FILE_PATH\n    Try 'slimm --help' for more information.\n\nVERSION\n\n    * SLIMM version: 0.3.0\n    * Last update: February 2018\n    \n\n### Downloads:\n\n#### Executables\nPre-built executables for Linux and Mac are made available at the [releases page]( https://github.com/seqan/slimm/releases/latest).\n\n#### Source code\nYou can build SLIMM from its source. Instruction on how to build from source can be found at the [slimm wiki] (https://github.com/seqan/slimm/wiki) \n\n#### Cite us\n\nIf you use SLIMM in your work-flows, don't forget to cite us.\n\nDadi TH, Renard BY, Wieler LH, Semmler T, Reinert K. (2017) SLIMM: species level identification of microorganisms from metagenomes. PeerJ 5:e3138 https://doi.org/10.7717/peerj.3138\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseqan%2Fslimm","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fseqan%2Fslimm","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fseqan%2Fslimm/lists"}