{"id":32563010,"url":"https://github.com/smithlabcode/zagros","last_synced_at":"2025-10-29T02:56:09.719Z","repository":{"id":16146758,"uuid":"18892344","full_name":"smithlabcode/zagros","owner":"smithlabcode","description":"Zagros is an algorithm for motif discovery in CLIP-seq data","archived":false,"fork":false,"pushed_at":"2014-11-04T22:29:30.000Z","size":1944,"stargazers_count":2,"open_issues_count":7,"forks_count":0,"subscribers_count":8,"default_branch":"master","last_synced_at":"2025-04-01T00:29:56.172Z","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":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/smithlabcode.png","metadata":{"files":{"readme":"README.TXT","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-04-17T20:23:12.000Z","updated_at":"2021-05-21T11:56:02.000Z","dependencies_parsed_at":"2022-09-03T00:00:54.495Z","dependency_job_id":null,"html_url":"https://github.com/smithlabcode/zagros","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/smithlabcode/zagros","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fzagros","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fzagros/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fzagros/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fzagros/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/smithlabcode","download_url":"https://codeload.github.com/smithlabcode/zagros/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2Fzagros/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":281549786,"owners_count":26520515,"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","status":"online","status_checked_at":"2025-10-29T02:00:06.901Z","response_time":59,"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":"2025-10-29T02:56:04.699Z","updated_at":"2025-10-29T02:56:09.709Z","avatar_url":"https://github.com/smithlabcode.png","language":"C++","readme":"\n                    ______                         \n                   |___  /                         \n                      / / __ _  __ _ _ __ ___  ___ \n                     / / / _` |/ _` | '__/ _ \\/ __|\n                    / /_| (_| | (_| | | | (_) \\__ \\\n                   /_____\\__,_|\\__, |_|  \\___/|___/\n                                __/ |              \n                               |___/               \n                   ********************************\n                   *            V1.1.0            *\n                   ********************************\n\n\n*********************************\nCopyright and License Information\n*******************************************************************************\nCopyright (C) 2013\nUniversity of Southern California,\nEmad Bahrami-Samani, Philip J. Uren, Andrew D. Smith\n  \nAuthors: Emad Bahrami-Samani, Philip J. Uren, Andrew D. Smith\n  \nThis program is free software: you can redistribute it and/or modify\nit under the terms of the GNU General Public License as published by\nthe Free Software Foundation, either version 3 of the License, or\n(at your option) any later version.\n  \nThis program is distributed in the hope that it will be useful,\nbut WITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\nGNU General Public License for more details.\n  \nYou should have received a copy of the GNU General Public License\nalong with this program.  If not, see \u003chttp://www.gnu.org/licenses/\u003e.\n\n\n***********************\nBuilding and Installing \n*******************************************************************************\nThis software package has been designed to operate in a UNIX-like environment.\nIt has been tested on MacOS X Snow Leopard and Linux. \n\nStep 0\n------\n  This software package requires a functioning installation of the GNU \n  Scientific Library (GSL). If you don't already have this installed, you \n  will need to download and install it from http://www.gnu.org/software/gsl/\n\nStep 1\n------\n  To build the binaries, type the following, where '\u003e' is your prompt and the\n  CWD is the root of the distribution  \n  \n  \u003e make all \n  \nStep 2\n------\n  To install the binaries, type the following, where '\u003e' is your prompt and the\n  CWD is the root of the distribution\n  \n  \u003e make install\n  \n  This will place the binaries in the bin directory under the package root.\n  They can be used directly from there without any additional steps. You can\n  add that directory to your PATH environment variable to avoid having to \n  specify their full paths, or you can copy the binaries to another directory\n  of your choice in your PATH \n  \n  \n***********\nBasic Usage\n*******************************************************************************\n\nZagros has four modes of operations.\n\n\n******************\n1.) Sequence only: \n\nIn this mode, only the sequence information is used for motif discovery. The \ninput can either be a set of sequences in fasta format or genomic regions in \nbed format. This set of regions/sequences corresponds to the locations of \nsignificant enrichment for reads in the experiment.\n\nIn case the input is the set of sequences, you can simply run:\n\n    \u003e ./zagros input.fa\n\nIf the input consists of a set of genomic regions, the set of the target genome\nsequences must also be provided to Zagros to extract the sequnces:\n\n    \u003e ./zagros -c path/to/chrom_directory input.bed\n\nThe chromosome directory can be downloaded from UCSC genome browser website.\nThe lastest versions can be found here:\nhttp://hgdownload.soe.ucsc.edu/downloads.html\n\n\n**************************\n2.) Sequence and Structure\n\nIn this mode, in addition to the target sequences the secondary structure information\nis used as well. In this case, the secondary structure data must be first obtained \nand saved using the \"thermo\" program:\n\n    \u003e ./thermo -o input.str input.fa\n\n    or\n\n    \u003e ./thermo -c path/to/chrom_directory -o input.str input.bed\n\nAfter this step, by providing both the target and secondary structure file to Zagros \nthe motif discovery is performed based on both.\n\n    \u003e ./zagros -t input.str input.fa\n\n    or\n\n    \u003e ./zagros -c path/to/chrom_directory -t input.str input.bed\n\n\n**********************************\n3.) Sequence and Diagnostic events\n\nIn this mode, in addition to the target sequences the information about cross-link\nmodification events is used as well. In this case, the diagnostic events information \nmust be first obtained and saved using the \"extractDEs\" program.\n\nThe input to extractDEs program is the set of mapped reads. The user must specify\nwhat technology is used for obtaining the reads (hCLIP, pCLIP or iCLIP), what mapper\nis used for mapping the reads, and the genomic regions of significant regions that\nis used for zagros as input. ExtractDEs then produces the set of diagnostic events \ncorrsponding to the regions of interest. Zagros can interprete the mapped reads from \nthree mappers: bowtie (native output format), novoalign (native output format) and \nRMAP (bed format).\n\n    \u003e ./extractDEs -m novoalign -t iCLIP -o input.des -r input.bed mapped_reads.novo\n\nThen run zagros program by inputing the diagnostic events file as one of the options.\n\n    \u003e ./zagros -d input.des input.fa\n\n    or\n\n    \u003e ./zagros -c path/to/chrom_directory -d input.des input.bed\n\n\n*********************************************\n4.) Sequence, Structure and Diagnostic events\n    \u003e ./thermo -o input.str input.fa\n    \u003e ./extractDEs -m novoalign -t iCLIP -o input.des -r mapped_reads.nov\n    \u003e ./zagros -t input.str -d input.des input.fa\n\n\n********************\nCommand Line Options\n*******************************************************************************\n\nUsage: zagros [OPTIONS] \u003ctarget_regions/sequences\u003e\n\nOptions:\n  -o, -output             output file name (default: stdout) \n  -w, -width              width of motifs to find (4 \u003c= w \u003c= 12; default: 6) \n  -n, -number             number of motifs to output (default: 1) \n  -c, -chrom              directory with chrom files (FASTA format) \n  -t, -structure          structure information file \n  -d, -diagnostic_events  diagnostic events information file \n  -i, -diagEventsThresh   down-sample diagnostic events to this many per \n                          sequence (-1 for no down-sampling; default: -1) \n  -s, -starting-points    number of starting points to try for EM search. Higher \n                          values will be slower, but more likely to find the \n                          global maximum. \n  -v, -verbose            print more run info \n\nHelp options:\n  -?, -help               print this help message \n      -about              print about message \n\n\n**************************************\n4. Input and output formats of Zagros\n*******************************************************************************\n\nZagros takes three possible inputs for mapped reads:\n  1.) RMAP      (BED format)              [REQUIRED if using diagnostic evnts]\n  2.) Novoalign (Novoalign native format) [REQUIRED if using diagnostic evnts]      \n  3.) Bowtie    (Bowtie native format)    [REQUIRED if using diagnostic evnts]\n\n\n************************\nContacts and bug reports\n*******************************************************************************\nEmad Bahrami-Samani \nbahramis@usc.edu\n\nPhilip J. Uren\nuren@usc.edu\n\nAndrew D. Smith\nandrewds@usc.edu\n\nIf you found a bug in Piranha, we'd like to know about it. Before contacting us\nthough, please check the following list:\n\n  1.) Are you using the latest version? The bug you found may already have \n      been fixed.\n  2.) Check that your input is in the correct format and you have selected\n      the correct options.\n  3.) Please reduce your input to the smallest possible size that still \n      produces the bug; we will need your input data to reproduce the \n      problem.\n\n\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmithlabcode%2Fzagros","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsmithlabcode%2Fzagros","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmithlabcode%2Fzagros/lists"}