{"id":24152636,"url":"https://github.com/peterhj/amos","last_synced_at":"2025-10-23T19:53:36.302Z","repository":{"id":22324768,"uuid":"25660187","full_name":"peterhj/amos","owner":"peterhj","description":null,"archived":false,"fork":false,"pushed_at":"2014-10-24T17:45:23.000Z","size":2208,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":0,"default_branch":"master","last_synced_at":"2025-06-03T20:06:18.000Z","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/peterhj.png","metadata":{"files":{"readme":"README","changelog":null,"contributing":null,"funding":null,"license":"COPYING","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-10-23T22:12:48.000Z","updated_at":"2014-10-24T17:45:25.000Z","dependencies_parsed_at":"2022-08-21T03:00:32.796Z","dependency_job_id":null,"html_url":"https://github.com/peterhj/amos","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/peterhj/amos","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/peterhj%2Famos","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/peterhj%2Famos/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/peterhj%2Famos/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/peterhj%2Famos/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/peterhj","download_url":"https://codeload.github.com/peterhj/amos/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/peterhj%2Famos/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":280683815,"owners_count":26372970,"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":"2025-10-23T02:00:06.710Z","response_time":142,"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":"2025-01-12T10:16:29.714Z","updated_at":"2025-10-23T19:53:36.284Z","avatar_url":"https://github.com/peterhj.png","language":"C++","funding_links":[],"categories":["Alignments"],"sub_categories":[],"readme":"Welcome to AMOS Assembler. A Modular Open Source Assembler.\nwebsite: \u003chttp://amos.sourceforge.net\u003e\ncontact: \u003camos-help@lists.sourceforge.net\u003e\n\n   AMOS is open source software. Please see the `COPYING' file for\ndetails. For documentation, please refer to the Documentation\nsection. For building and installation instructions please see the\nInstallation section.\n\n\nBrief Summary\n=============\n\n   The AMOS consortium is committed to the development of open-source\nwhole genome assembly software. The project acronym (AMOS) represents\nour primary goal -- to produce A Modular, Open-Source whole genome\nassembler. Open-source so that everyone is welcome to contribute and\nhelp build outstanding assembly tools, and modular in nature so that\nnew contributions can be easily inserted into an existing assembly\npipeline. This modular design will foster the development of new\nassembly algorithms and allow the AMOS project to continually grow and\nimprove in hopes of eventually becoming a widely accepted and deployed\nassembly infrastructure. In this sense, AMOS is both a design\nphilosophy and a software system.\n\n   Because of its modular nature, AMOS cannot be described in one\nparagraph since it is a composite of many different systems. See the\nPipeline section for quick descriptions of each pipeline, or the\nDocumentation section on where to find comprehensive documentation.\n\n\nInstallation\n============\n\n   Please follow the instructions in the `INSTALL' file for building\nand installation. The `INSTALL' file is only a generic installation\ndocument, so any AMOS specific installation notes are listed below.\n\n   Once `make install' is issued, the installed scripts and Perl\nmodules must not be moved. Thus, convince yourself of the installation\ndirectory beforehand and set the $PREFIX variable for `configure'\naccordingly. AMOS makes use of a few custom installation directories\nnot mentioned in `INSTALL', they are as follows. $datadir, $libdir and\n$includedir are set by `configure', see `configure --help' for more\ninformation.\n\n   - Documentation will be installed in $datadir/doc/amos-[version]\n   - AMOS libraries and Perl modules will be installed in $libdir/AMOS\n   - TIGR libraries and Perl modules will be installed in $libdir/TIGR\n   - AMOS headers will be installed in $includedir/AMOS\n   - TIGR headers will be installed in $includedir/TIGR\n\n  In addition, certain parts of the AMOS package require the X\nwindowing system along with the Qt libraries. Parameters for these\npackages may be modified with the following options:\n\n   --x-includes=DIR      X include files are in DIR\n   --x-libraries=DIR     X library files are in DIR\n   --with-x              use the X Window System\n   --with-Boost-dir=DIR  Directory in which to find the ./boost folder for the\n                         Boost toolkit\n   --with-qmake-qt4=DIR  Path to qmake using Qt version 4.x\n\nPlease see the INSTALL file for more information and Cygwin and OS X\nspecific instructions.\n\nDependencies\n============\n\n   The AMOS package makes use of Python and Perl (Practical Extraction\nand Report Language). Python and Perl are available on most systems\nand the latest versions can be downloaded free of charge. AMOS\nrequires Perl version 5.6.0 or later. If `perl' or `python' are\navailable from your system PATH, all is well, if not you will need to\ninstruct `configure' where they are located by setting the\nenvironment variable PERL and PYTHON to the full path of `perl' and\n`python' respectively (see the Defining Variables section in the\n`INSTALL' file). Some Perl scripts in the AMOS package require\nadditional modules that you should install:\n   DBI (http://search.cpan.org/~timb/DBI/)\n   Statistics::Descriptive (http://search.cpan.org/~shlomif/Statistics-Descriptive-3.0100/)\n   XML::Parser (http://search.cpan.org/~msergeant/XML-Parser-2.36/)\n\n   AMOScmp and minimus2 make use of the NUCmer whole genome alignment\nutility which is part of the MUMmer package. If you wish to run AMOScmp,\nyou will need download and install MUMmer (available for free from\n\u003chttp://mummer.sourceforge.net\u003e). If `nucmer' is available from\nyour system PATH, all is well, if not you will need to instruct\n`configure' where it is located by setting the environment variable\nNUCMER to the full path of `nucmer' (see the Defining Variables\nsection in the `INSTALL' file).\n\n   The validation pipeline `amosvalidate' also depends on Nucmer, but\nit is not essential to the validation process. If you wish to run\namosvalidate without the \"alignment breakpoints\" step, comment out\nsteps 600-710 with '#' in the `amosvalidate' script.\n\n   The minimus2-blat pipeline relies on BLAT instead of nucmer.\n\n   The AMOS assembly viewer Hawkeye relies on X windows and the Qt4 \ntoolkit. Note that the Qt toolkit is somewhat volatile, so it is \nimportant to install Qt4 and not a newer or older version. If Qt is not \ncentrally installed on your system, you will need to do so to make \nuse of this graphical viewer. The configure script should be able \nto identify most standard Qt installations, however you may need \nto set the `--with-qmake-qt4' configure option to the location of \nyour Qt package. If all else fails, you may have to build the\nviewer independently. If so, make AMOS without hawkeye, and then\ncd into the src/hawkeye directory, run 'qmake', and then 'make'.\n\n\nDocumentation\n=============\n\n   Basic documentation for the individual pipelines is located in the\n`doc' subdirectory. Comprehensive documentation can be found on\nthe AMOS website \u003chttp://amos.sourceforge.net\u003e.\n\n\nPipeline\n========\n\n   Listed here are the current AMOS pipelines available. Source files\nfor the pipelines are in `src/Pipeline' and will be installed in\n$bindir as executable scripts. Please see individual documentation for\neach pipeline in the `doc' directory.\n\n   - minimus -\n   Minimus is an assembly pipeline designed specifically for small\n   data-sets, such as the set of reads covering a specific gene. Note\n   that the code will work for larger assemblies (we have used it to\n   assemble bacterial genomes), however, due to its stringency, the\n   resulting assembly will be highly fragmented.  For large and/or\n   complex assemblies the execution of Minimus should be followed by\n   additional processing steps, such as scaffolding.\n\n   - Minimo -\n   Minimo uses the same assembly strategy as minimo but offers more\n   flexibility in the sequence input, output and processing.\n\n   - minimus2 \n   minimus2 is an assembly pipeline designed for merging two sequence sets\n   (Example: the contigs generated by two assembly processes)\n   It uses a nucmer based overlap detector instead of the hash-overlap program \n   used by the minimus pipeline. \n\n   - minimus2-blat\n   This pipeline performs the same function as minimus2, but uses BLAT instead\n   of nucmer for the alignments, which provides a speedup.\n\n   - AMOScmp -\n   AMOScmp provides a general overlap-layout-consensus pipeline for\n   assembly, but with a twist. The overlap phase of the process is\n   replaced with an alignment to a reference, i.e. all sequencing reads\n   are aligned to a finished reference sequence and their alignments are\n   used to determine their layout position.\n\n   - AMOScmp-shortReads -\n   Modified version AMOScmp for assembling short reads\n   Differences compared to AMOScmp:\n     * smaller nucmer alignment cluster size (20 vs 65)\n     * smaller make-consensus alignment wiggle value (2 vs 15)\n\n   - AMOScmp-shortReads-alignmentTrimmed -\n   Very similar to AMOScmp-shortReads but it does a reference based alignment \n   trimming of the reads prior to the assembly. \n   Differences compared to AMOScmp-shortReads:\n     * aligns the reads to reference using nucmer\n     * determines zero coverage regions\n     * extracts the read clear ranges from the alignment(delta) file\n     * exrtends the read clear ranges for reads adjacent to zero coverage regions\n     * updates the bank with the new clear ranges\n     * updates the alignment(delta) file with the new read lengths and clear ranges\n\n   - goBambus2 -\n   goBambus2 is a pipeline to drive the Bambus2 modules, designed to\n   scaffold polymorphic and metagenomic data\n\n   - amosvalidate -\n   Amosvalidate is a validation pipeline for genome assemblies. This\n   pipeline includes a collection of methods for ascertaining the\n   quality of an assembly, and examines multiple measures of assembly\n   quality to pinpoint potential mis-assemblies. Validation techniques\n   include mate-pair validation, repeat analysis, coverage analysis,\n   identification of correlated read polymorphisms, and read alignment\n   breakpoint analysis. Regions of the assembly exhibiting multiple\n   signatures of mis-assembly are flagged as suspicious and output by\n   amosvalidate for further examination.\n\n   - hawkeye -\n   Hawkeye is a visual analytics tool for genome assembly analysis and\n   validation, designed to aid in identifying and correcting assembly\n   errors. Hawkeye blends the best practices from information and\n   scientific visualization to facilitate inspection of large-scale\n   assembly data while minimizing the time needed to detect\n   mis-assemblies and make accurate judgments of assembly quality.\n\n\nAugust 2011\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpeterhj%2Famos","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpeterhj%2Famos","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpeterhj%2Famos/lists"}