{"id":19863545,"url":"https://github.com/sandialabs/tiger","last_synced_at":"2025-05-02T04:31:11.557Z","repository":{"id":59424298,"uuid":"223024318","full_name":"sandialabs/TIGER","owner":"sandialabs","description":"Target / Integrative Genetic Element Retriever: precisely maps IGEs (a defined type of genomic island) in bacterial and archaeal genomes; package also includes orthogonal program Islander","archived":false,"fork":false,"pushed_at":"2025-02-11T23:57:47.000Z","size":47997,"stargazers_count":13,"open_issues_count":4,"forks_count":5,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-04-06T22:38:43.649Z","etag":null,"topics":["bioinformatics","perl","scr-1633","scr-2281","snl-other"],"latest_commit_sha":null,"homepage":"","language":"Perl","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/sandialabs.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}},"created_at":"2019-11-20T20:45:57.000Z","updated_at":"2025-03-23T14:47:19.000Z","dependencies_parsed_at":"2024-01-16T08:55:05.710Z","dependency_job_id":"f85acc30-157f-4f3f-a6cf-add63327af24","html_url":"https://github.com/sandialabs/TIGER","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sandialabs%2FTIGER","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sandialabs%2FTIGER/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sandialabs%2FTIGER/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sandialabs%2FTIGER/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sandialabs","download_url":"https://codeload.github.com/sandialabs/TIGER/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":251986787,"owners_count":21675951,"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":["bioinformatics","perl","scr-1633","scr-2281","snl-other"],"created_at":"2024-11-12T15:15:06.708Z","updated_at":"2025-05-02T04:31:06.548Z","avatar_url":"https://github.com/sandialabs.png","language":"Perl","funding_links":[],"categories":[],"sub_categories":[],"readme":"# TIGER version 2\nTarget / Integrative Genetic Element Retriever, version 2\n\n# Citation\nMageeney CM, Lau BY, Wagner JW, Hudson CM, Schoeniger JS, Krishnakumar R and Williams KP. 2020. New candidates for regulated gene integrity revealed through precise mapping of integrative genetic elements. Nucleic Acids Research 48(8):4052-4065 (doi.org/10.1093/nar/gkaa156)\nMageeney CM, Trubl G, Williams KP. 2022. Improved mobilome delineation in fragmented genomes. Front Bioinform doi: 10.3389/fbinf.2022.866850\n\n# INSTALLATION\ngit clone -b TIGER2 https://github.com/sandialabs/TIGER.git\n\nUser should have a reference genome blast database available, such as refseq_genomic\n\nUser should download Pfam-A.hmm from pfam and place it or a symbolic link to it in the TIGERPATH/db directory\n\n```ln -s /ABSOLUTE_PATH/Pfam-A.hmm PATH_TO_TIGER/db/Pfam-A.hmm```\n\nThe following programs (with suggested versions) must be properly installed and in the user's path:\n* blastn, blastdbcmd, makeblastdb 2.6.0+\n* prokka 1.11\n* bedtools 2.27.1\n* tRNAscan-SE 2.0.2\n* cmscan 1.1.2\n* Perl Core: List::Util, File::Spec, Cwd, Getopt::Long\n* Perl Noncore: IPC::Run3\n\n# RUNNING\nRequires a .fa file in the same folder with the same prefix.\nYou may add a .tax file to specify what the genome is.\nThe tab-separated fields of the one-line .tax file are: \n 1. taxid\n 2. organism\n 3. Division;Phylum;Class;Order;Family;Genus;Species\n 4. Genetic code (see https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi)\n 5. Nickname (short name for organism, eg Eco837 for the 837th E. coli genome)\n\n## Sample calls to try within /testdata (PATH: to TIGER installation; DB: to reference genome blast database)\n\n```perl PATH/bin/islander.pl -verbose genome.fa \u0026\u003e islander.log```\n\n```perl PATH/bin/tiger.pl -verbose -db DB -cross simple -fasta genome.fa \u0026\u003e tiger.log```\n\n```perl PATH/bin/resolve.pl mixed lenient genome genome.island.merge.gff islander.gff \u0026\u003e resolve.log```\n\n```perl PATH/bin/typing.pl resolved.gff \u0026\u003e typing.log```\n\n```perl PATH/bin/typing.pl genome.island.nonoverlap.gff \u0026\u003e typing.log```\n\n## Notes:\nbefore rerunning islander.pl: ```rm genome.stats```\n\nbefore rerunning tiger.pl: ```rm genome.island.nonoverlap.gff```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsandialabs%2Ftiger","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsandialabs%2Ftiger","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsandialabs%2Ftiger/lists"}