{"id":15050909,"url":"https://github.com/debian/fastx-toolkit","last_synced_at":"2025-10-04T13:32:00.161Z","repository":{"id":146912428,"uuid":"14250247","full_name":"Debian/fastx-toolkit","owner":"Debian","description":"FASTA/FASTQ pre-processing programs","archived":false,"fork":true,"pushed_at":"2014-01-13T00:26:01.000Z","size":3900,"stargazers_count":5,"open_issues_count":0,"forks_count":3,"subscribers_count":16,"default_branch":"debian/unstable","last_synced_at":"2024-09-30T02:23:06.788Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"C","has_issues":false,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":"agordon/fastx_toolkit","license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/Debian.png","metadata":{"files":{"readme":"README","changelog":"ChangeLog","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":"2013-11-09T03:16:20.000Z","updated_at":"2024-09-26T12:10:39.000Z","dependencies_parsed_at":"2023-03-24T23:12:39.768Z","dependency_job_id":null,"html_url":"https://github.com/Debian/fastx-toolkit","commit_stats":null,"previous_names":[],"tags_count":18,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Debian%2Ffastx-toolkit","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Debian%2Ffastx-toolkit/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Debian%2Ffastx-toolkit/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Debian%2Ffastx-toolkit/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Debian","download_url":"https://codeload.github.com/Debian/fastx-toolkit/tar.gz/refs/heads/debian/unstable","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":235258222,"owners_count":18961320,"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":"2024-09-24T21:29:44.230Z","updated_at":"2025-10-04T13:31:54.778Z","avatar_url":"https://github.com/Debian.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"FASTX-Toolkit\n=============\n\n\nShort Summary\n===============\n\nThe FASTX-Toolkit is a collection of command line tools for Short-Reads \nFASTA/FASTQ files preprocessing.\n\n\n\nMore Details\n==============\n\nNext-Generation sequencing machines usually produce FASTA or FASTQ files, \ncontaining multiple short-reads sequences (possibly with quality information).\n\nThe main processing of such FASTA/FASTQ files is mapping (aka aligning)\nthe sequences to reference genomes or other databases using specialized\nprograms. \n\nExample of such mapping programs are:\nBlat (http://www.kentinformatics.com/index.asp), \nSHRiMP (http://compbio.cs.toronto.edu/shrimp),\nLastZ (http://www.bx.psu.edu/miller_lab),\nMAQ (http://maq.sourceforge.net/)\nAnd many many others.\n\nHowever, \nIt is sometimes more productive to preprocess the FASTA/FASTQ files before \nmapping the sequences to the genome - manipulating the sequences to \nproduce better mapping results.\n\nThe FASTX-Toolkit tools perform some of these preprocessing tasks.\n\n\n\nAvailable Tools\n===============\n\nFASTQ-to-FASTA - Converts a FASTQ file to a FASTA file..\n\nFASTQ-Statistics - scans a FASTQ file, and produces some statistics about the \n\tquality and the sequences in the file.\n\t\nFASTQ-Quality-BoxPlot, and\nFASTQ-Nucleotides-Distribution - Generates charts based on the statistics \n\tgenerated by FASTQ-Statistics. These charts can be used to quickly\n\tsee the quality of the sequenced library.\n\t\nFASTQ-Quality-Converter - Converts from ASCII to numeric quality scores.\n\nFASTQ-Quality-Filter - removes low-quality sequences from FASTQ files.\n\nFASTX-Artifacts-Filter - removes some sequencing artifacts from FASTA/Q files.\n\nFASTX-Barcode-Splitter - A common practice is to sequence multiple biological\n\tsamples in the same library (marking each sample using a dedicated \n\tbarcode). The resulting FASTA/Q file contains intermixed sequences \n\tfrom those samples. This tool separates FASTA/Q files into several \n\tindividual files, based on the barcodes.\n\t\nFASTX-Clipper - Adapters (aka Linkers) are added to the library (before \n\tsequencing), and should be removed from the resulting FASTA/Q file.\n\tThis tool removes (clips) adapters.\n\t\nFASTA-Clipping-Histogram - After clipping a FASTA file, this tool generates a\n\tchart showing the length of the clipped sequences.\n\t\nFASTX-Reverse-Complement - Produces a reverse-complement of FASTA/Q file.\n\tIf a FASTQ file is given, the quality scores are also reversed.\n\t\nFASTX-Trimmer - Extract sub-seqeunces from FASTA/Q file. Two examples are:\n\tRemoving barcodes from the 5'-end of all sequences in a FASTQ file;\n\tCutting 7 nucleotides from the 3'-end of all sequences in a FASTA file.\n\n\n\nGalaxy\n======\n\nGalaxy (http://g2.bx.psu.edu) is web-based framework for computational biology.\n\nWhile the programs in the FASTX-Toolkit are command-line based, the package \ninclude the necessary files to integrate the tools into a Galaxy server,\nAllowing users to execute this tools from their web-browser.\n\nIf you run your own local mirror of a Galaxy server, you can integrate the\nFASTX-Toolkit into your Galaxy server.\n\n\n\nSoftware Requirements\n=====================\n\n1. GCC is required to compile most tools.\n\n2. FASTA-Clipping-Histogram tool requires Perl, the \"PerlIO::gzip\",\n   \"GD::Graph::bars\" modules.\n   \n   Installing the perl modules can be accomplised by running:\n\n   $ sudo cpan 'PerlIO::gzip'\n   $ sudo cpan 'GD::Graph::bars'\n   \n3. FASTX-Barcode-Splitter requires the GNU Sed program.\n   \n4. FASTQ-Quality-Boxplot and FASTQ-Nucleotides-Distribution requires the\n   'gnuplot' program.\n\n\nInstallation\n============\n\nTo compile to tools, run:\n\n  $ ./configure\n  $ make\n  \nTo install the tools, run (as root):\n\n  $ sudo make install\n\nThis will install the tools into /usr/local/bin.\nTo install the tools to a different location, change the 'configure' step to:\n\n  $ ./configure --prefix=/DESTINATION/DIRECTORY\n  \n\n\nCommand Line Usage\n==================\n\nMost tools support \"-h\" argument to show a short help screen.\nBetter documentation is not available at this moment.\nSome more details and examples are available in the \u003chelp\u003e section\nof the XML tool files (in the 'galaxy' subdirectory).\n  \n \nGalaxy Installation\n===================\n\nGalaxy Installation should be done manually, and requires technical\nunderstading of the Galaxy framework.\n\n1. build and install the command line tools (as described above).\n\n2. Make backup of your galaxy installation (better safe than sorry).\n\n3. Run the 'install_galaxy_files.sh' script, \n   and specify the galaxy root directory.\n   This script copies the files from the 'galaxy' sub-directory into\n   your galaxy mirror directory.\n   \n4. Manually add the content of ./galaxy/fastx_toolkit_conf.xml file,\n   into your Galaxy's tool_conf.xml\n   \n5. Edit [YOUR-GALAXY]/tool-data/fastx_clipper_sequences.txt file,\n   And add your custom adapters/linkers.\n   \n6. Modify the \"fastx_barcode_splitter_galaxy_wrapper.sh\" as explained\n   Below (see section \"Special configuration for Barcode-Splitter\").\n\n7. Restart Galaxy.\n\nAlways make backup of your galaxy server files before trying to install \nthe FASTX-Toolkit. \n\n\n\nGalaxy Testing\n==============\n\nThe following tools support Galaxy's functional testing:\n(Run from Galaxy's main directory)\n  $ sh run_functional_tests.sh -id cshl_fastq_qual_conv\n  $ sh run_functional_tests.sh -id cshl_fastq_to_fasta\n  $ sh run_functional_tests.sh -id cshl_fastq_qual_stat\n  $ sh run_functional_tests.sh -id cshl_fastx_trimmer\n  $ sh run_functional_tests.sh -id cshl_fastx_reverse_complement\n  $ sh run_functional_tests.sh -id cshl_fastx_artifacts_filter\n  $ sh run_functional_tests.sh -id cshl_fasta_collapser\n  $ sh run_functional_tests.sh -id cshl_fastx_clipper\n \n\nSpecial configuration for Barcode-Splitter\n==========================================\n\nWhen running the barcode-splitter tool from the command line you specify a \nprefix direcotry - the output files will be written to that directory (similar\nto GNU's split program usage).\n\nRunning the barcode-splittter inside galaxy requires a special hack beacuse\n(I don't know how to|Galaxy can't) create a variable number of output datasets.\nThe number of required output files is determined by the tool only AFTER reading \nthe barcodes description file.\n\nThe Galaxy-version of Barcode-Splitter works like this:\n1. A FASTA/FASTQ file, and a Barcode description file are fed to the tool.\n2. The tool produces a single output dataset (inside galaxy). This output\n   is an HTML file, containing links to the split FASTA files.\n3. Users can use the links to get the split FASTA files.\n   (Since Galaxy's 'upload data' tool accepts URLs, this is not a real problem).\n   \n4. As the galaxy administrator, you'll have to edit \n   'fastx_barcode_splitter_galaxy_wrapper.sh' script and change BASEPATH and \n   PUBLICURL to point to a publicly accesibly path on your server.\n   \nExample:\n\nfastx_barcode_splitter_galaxy_wrapper.sh contains:\n\n   BASEPATH=\"/media/sdb1/galaxy/barcode_splits/\"\n   PUBLICURL=\"http://tango.cshl.edu/barcode_splits/\"\n\nWhen a user runs the barcode splitter tool, the FASTA files will be generated in \n\"/media/sdb1/galaxy/barcode_splits/\".  \nThe URL \"http://tango.cshl.edu/barcode_splits\" is set (in an apache server) to\nserve files from \"/media/sdb1/galaxy/barcode_splits/\", with the following \nconfiguration:\n\n    Alias /barcode_splits \"/media/sdb1/galaxy/barcode_splits/\"\n    \u003cDirectory \"/media/sdb1/galaxy/barcode_splits/\"\u003e\n        AllowOverride None\n        Order allow,deny\n        Allow from all\n    \u003c/Directory\u003e\n\n\n\n\nLicenses\n========\n\nFASTX-Toolkit is distributed under the Affero GPL version 3 or later (AGPLv3),\n\nEXCEPT\n\nAll files under the 'galaxy' sub-directory are distributed under the\nsame license as Galaxy itself (which is an MIT-style license).\n\n\nWhile IANAL, these licenses basically mean that:\n1. You're free to use FASTX-toolkit,\n\n2. You're free to integrate FASTX-toolkit in your Galaxy mirror server \n   (or any other server).\n   \n3. You're free to modify the files under 'galaxy',\n   without making your modifications public.\n   \n4. If you modify the FASTX-toolkit tools, and make those modifications \n   publicly available (either as downloadable tools, part of another product),\n   or as a web-based server - you must make the modified source code freely \n   available (free as in speech).\n   \nSee the COPYING file for the full Affero GPL.\nSee the GALAXY-LICENSE file for galaxy's license.\n\nPlease remember: \n  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY\nAPPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT\nHOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM \"AS IS\" WITHOUT WARRANTY\nOF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,\nTHE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR\nPURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM\nIS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF\nALL NECESSARY SERVICING, REPAIR OR CORRECTION.\n\n\n=============\nPlease send all comments, suggestions, bug reports (or better yet - bug fixes)\nto assafgordon@gmail.com .\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdebian%2Ffastx-toolkit","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fdebian%2Ffastx-toolkit","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fdebian%2Ffastx-toolkit/lists"}