{ "info": { "author": "Postlethwait Lab, University of Oregon", "author_email": "postlethwait.lab@gmail.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 5 - Production/Stable", "Intended Audience :: Science/Research", "License :: Free for non-commercial use", "Programming Language :: Python :: 2", "Programming Language :: Python :: 2.7", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.4", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "Duplig\u00e4nger\n===========\n\n*Duplig\u00e4nger* is a reference-based, UMI-aware, 5'-trimming-aware PCR duplicate\nremoval pipeline.\n\nUsage: dupliganger [options] [...]\n\n\n*Duplig\u00e4nger* is a pipeline. Each stage of the pipeline is run by passing a\n'command' to *Duplig\u00e4nger*. The commands / pipeline-steps (in order) are as\nfollows::\n\n remove-umi 1. Annotate read names with UMIs (clip inline UMIs if needed).\n remove-adapter 2. Remove adapters ('Cutadapt' wrapper).\n qtrim 3. Quality trim ('Trimmomatic' wrapper).\n annotate-qtrim 4. Annotates quality trimmed file(s).\n align 5. Align reads to a reference genome assembly (performed manually by user).\n dedup 6. Use the alignment to remove PCR duplicates.\n\nWhile generally used only by the developers of *Duplig\u00e4nger*, the 'dedup'\ncommand is comprised of the following *Duplig\u00e4nger* commands run in the\nfollowing order::\n\n build-read-db 1. Build a database of aligned reads.\n build-location-db 2. Build a database of locations of aligned reads.\n build-dup-db 3. Build a database of PCR duplicates.\n\nOptions::\n\n -o OUT_DIR Place results in directory OUT_DIR.\n --compress Compress output.\n\nNote:\n *Duplig\u00e4nger* supports (and autodetects) input FASTQ files that are gzipped.\n\nSee 'dupliganger help ' for more information on a specific command.\n\nDocumentation\n=============\n\nFor further information on *Duplig\u00e4nger*, please see the full documentation at\nhttps://github.com/uoregon-postlethwait/dupliganger\n\nAuthors\n=======\n\n* Jason Sydes - Conceptual Design and Software Engineering\n* Peter Batzel - Conceptual Design\n* John H. Postlethwait - Project Advisor\n\nFunding\n=======\n\n*Duplig\u00e4nger* has been funded by the following grants:\n\n* NIH R01 OD011116 - Resources for Teleost Gene Duplicates and Human Disease\n* NIH R24 OD011199 - Advancing the Scientific Potential of Transcriptomics in Aquatic Models\n* NIH R24 OD018555 - Development of Aquatic Model Resources for Therapeutic Screens\n* NSF PLR-1543383 - Antarctic Fish and MicroRNA Control of Development and Physiology \n", "description_content_type": "", "docs_url": null, "download_url": "", "downloads": { "last_day": -1, "last_month": -1, "last_week": -1 }, "home_page": "https://github.com/uoregon-postlethwait/dupliganger", "keywords": "bioinformatics", "license": "LICENSE.txt", "maintainer": "", "maintainer_email": "", "name": "dupliganger", "package_url": "https://pypi.org/project/dupliganger/", "platform": "", "project_url": "https://pypi.org/project/dupliganger/", "project_urls": { "Homepage": "https://github.com/uoregon-postlethwait/dupliganger" }, "release_url": "https://pypi.org/project/dupliganger/0.98/", "requires_dist": null, "requires_python": "", "summary": "A reference-based, UMI-aware, 5\u02b9-trimming-aware PCR duplicate removal pipeline.", "version": "0.98" }, "last_serial": 5294555, "releases": { "0.92": [ { "comment_text": "", "digests": { "md5": "ce78d0696a7a9ebf72f6d4cadb1800f7", "sha256": "d17619321ca1beb92c0a53a34cdb85cb0971d6f1df36529922227288137d481f" }, "downloads": -1, "filename": "dupliganger-0.92-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "ce78d0696a7a9ebf72f6d4cadb1800f7", "packagetype": "bdist_wheel", "python_version": "py2.py3", "requires_python": ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4", "size": 154382, "upload_time": "2019-01-02T23:49:50", "url": "https://files.pythonhosted.org/packages/b1/a5/e4f0ae7bf23401ea97a6486144095eb5c13ee54a5d9bb390f19db423717a/dupliganger-0.92-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "6f41fa710ba14226ac681b101143b366", "sha256": "04703a39358a1157fe3a0af5eca243b2ceb892a49551f6033b67b81320e46e91" }, "downloads": -1, "filename": "dupliganger-0.92.tar.gz", "has_sig": false, "md5_digest": "6f41fa710ba14226ac681b101143b366", "packagetype": "sdist", "python_version": "source", "requires_python": ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4", "size": 91306, "upload_time": "2019-01-02T23:49:53", "url": "https://files.pythonhosted.org/packages/99/73/95985d31aef975a99048cdafbad54190451bafe70f325c8c80474b543d50/dupliganger-0.92.tar.gz" } ], "0.92.dev0": [ { "comment_text": "", "digests": { "md5": "2f23f4dbe16b527a20ca3aae256fc0d0", "sha256": "494824c9b944f7e9e74180f72a23dc6b9e1b8ae8a9322b010f1ad286e099a3bc" }, "downloads": -1, "filename": "dupliganger-0.92.dev0-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "2f23f4dbe16b527a20ca3aae256fc0d0", "packagetype": "bdist_wheel", "python_version": "py2.py3", "requires_python": ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4", "size": 61615, "upload_time": "2019-01-02T23:55:46", "url": "https://files.pythonhosted.org/packages/a3/2b/ad8571a49616a406ff83cb99267e916fd34391881fc252397e6fb6da7a60/dupliganger-0.92.dev0-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "d94d6aa90e8aae8984d34241ebc96f53", "sha256": "f6cd0f5f98348385a77ae6e3965f09f997d10cd717217814aace4cbace62a729" }, "downloads": -1, "filename": "dupliganger-0.92.dev0.tar.gz", "has_sig": false, "md5_digest": "d94d6aa90e8aae8984d34241ebc96f53", "packagetype": "sdist", "python_version": "source", "requires_python": ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4", "size": 76460, "upload_time": "2019-01-02T23:55:48", "url": "https://files.pythonhosted.org/packages/3a/a1/bd76864ec516bf94be39687f53c12eb4dd17635f08f4a31c5bcfd06b6940/dupliganger-0.92.dev0.tar.gz" } ], "0.93": [ { "comment_text": "", "digests": { "md5": "7675cb1b8405e588ea8743bc3a65839c", "sha256": "8c6a441ea87e03ba75d9ae1a4a78af6751aad27602766e7a2554b4776fc4d7ab" }, "downloads": -1, "filename": "dupliganger-0.93-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "7675cb1b8405e588ea8743bc3a65839c", "packagetype": "bdist_wheel", "python_version": "py2.py3", "requires_python": ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4", "size": 61533, "upload_time": "2019-01-03T00:10:19", "url": "https://files.pythonhosted.org/packages/82/5d/5295796b91acf9e92ecc64ff2892b95a55ad09cd4a980eb9be2e6ebba977/dupliganger-0.93-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "739ef871d49a21ea636c7c1eafb46812", "sha256": "72938b10623048d1441e3cea7a3a072321516c5c25e23e8c21d04430ac44322a" }, "downloads": -1, "filename": "dupliganger-0.93.tar.gz", "has_sig": false, "md5_digest": "739ef871d49a21ea636c7c1eafb46812", "packagetype": "sdist", "python_version": "source", "requires_python": ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4", "size": 75931, "upload_time": "2019-01-03T00:10:21", "url": "https://files.pythonhosted.org/packages/ed/84/3cf89dc7854d3e454ad1976e25fd883cf75676d43f2c76dbc2ef7ec0aac9/dupliganger-0.93.tar.gz" } ], "0.94": [ { "comment_text": "", "digests": { "md5": "3c0e1ed92957ca29079a23880c966d59", "sha256": "46a0b5c133c21669b431dc1f3e3829ccc16710998c35f78e25706c9f9bdd0d1a" }, "downloads": -1, "filename": "dupliganger-0.94-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "3c0e1ed92957ca29079a23880c966d59", "packagetype": "bdist_wheel", "python_version": "py2.py3", "requires_python": ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4", "size": 79490, "upload_time": "2019-01-03T00:50:10", "url": "https://files.pythonhosted.org/packages/a9/90/0fccec0722fd89ba2e717b1e0a3160ff7dcbf9e37be8529217734a9f7880/dupliganger-0.94-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "c0d8001b521b3399ea9aa8b42f71fc96", "sha256": "eb5f7ee86760e22dc7be99c57868ccf5dacd9bea7959d56004c89e849cb55cd6" }, "downloads": -1, "filename": "dupliganger-0.94.tar.gz", "has_sig": false, "md5_digest": "c0d8001b521b3399ea9aa8b42f71fc96", "packagetype": "sdist", "python_version": "source", "requires_python": ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4", "size": 91345, "upload_time": "2019-01-03T00:50:12", "url": "https://files.pythonhosted.org/packages/a8/53/7ebd4ccb57f6d5fcda8a79c05306dd643012c390ddbdc8456df48a07a119/dupliganger-0.94.tar.gz" } ], "0.95": [ { "comment_text": "", "digests": { "md5": "b58d39071f5d061c5bd1e4187d38251d", "sha256": "ddb2df352e6ea7808e0b8f65ad02b30d837ff3e29c333ea7bdfdcca891a8cd42" }, "downloads": -1, "filename": "dupliganger-0.95-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "b58d39071f5d061c5bd1e4187d38251d", "packagetype": "bdist_wheel", "python_version": "py2.py3", "requires_python": ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4", "size": 61534, "upload_time": "2019-01-03T01:14:41", "url": "https://files.pythonhosted.org/packages/54/54/baf32280191f60cc4ba02e2ec2b40720294dddad427ab2e483119cb9febc/dupliganger-0.95-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "304dbd12d41920523ef5f410c0ab3df1", "sha256": "251c543a2683cec23a64d3cc00d0492b55391b1bdd4a731a8752137bd94a4237" }, "downloads": -1, "filename": "dupliganger-0.95.tar.gz", "has_sig": false, "md5_digest": "304dbd12d41920523ef5f410c0ab3df1", "packagetype": "sdist", "python_version": "source", "requires_python": ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4", "size": 76004, "upload_time": "2019-01-03T01:14:43", "url": "https://files.pythonhosted.org/packages/d5/08/0cbe6bc97daa79311af8fc32f4375e9e590654017d5464cc4dfdc46fd78f/dupliganger-0.95.tar.gz" } ], "0.96": [ { "comment_text": "", "digests": { "md5": "dfa0605c8ac4e3320899ad92b772811b", "sha256": "c11c137611c5fc9177dfebbeb9c41e339a4d63fa3ab5a5eed36edb11d5f918fd" }, "downloads": -1, "filename": "dupliganger-0.96-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "dfa0605c8ac4e3320899ad92b772811b", "packagetype": "bdist_wheel", "python_version": "py2.py3", "requires_python": ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4", "size": 61532, "upload_time": "2019-01-03T01:45:25", "url": "https://files.pythonhosted.org/packages/d3/6b/e10cd9cb3a895a2219564370c14c012d2ba60d30925813cc4aaff53f1a0e/dupliganger-0.96-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "987709e492064d8359e5bd1331b51e80", "sha256": "fba3e6f8bd235c3b3475d7190ba28894fadf869e4c18dba52b781e74c492bc75" }, "downloads": -1, "filename": "dupliganger-0.96.tar.gz", "has_sig": false, "md5_digest": "987709e492064d8359e5bd1331b51e80", "packagetype": "sdist", "python_version": "source", "requires_python": ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4", "size": 76145, "upload_time": "2019-01-03T01:45:27", "url": "https://files.pythonhosted.org/packages/ad/19/7abb2f0997c4bbf4844bce5c570ecb1654dda0878f39c716afc850eba606/dupliganger-0.96.tar.gz" } ], "0.97": [ { "comment_text": "", "digests": { "md5": "8d48957926154b77500c4e486f55cb1f", "sha256": "76dded9fd048aac7c74a4f0b4d9d577ae33f31c31294455e54cf5e72a68fa57b" }, "downloads": -1, "filename": "dupliganger-0.97-py2.py3-none-any.whl", "has_sig": false, "md5_digest": "8d48957926154b77500c4e486f55cb1f", "packagetype": "bdist_wheel", "python_version": "py2.py3", "requires_python": ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4", "size": 62151, "upload_time": "2019-01-03T23:51:09", "url": "https://files.pythonhosted.org/packages/93/6a/50948527ae548384ecf499febf8d815dae0326a5f44a5c898841383de93d/dupliganger-0.97-py2.py3-none-any.whl" }, { "comment_text": "", "digests": { "md5": "8dbe147182fb01055bb1fa15298826b7", "sha256": "6d191636b867122ad10c8247970079dbb6e39c56e80b8232779ac424ad1b73aa" }, "downloads": -1, "filename": "dupliganger-0.97.tar.gz", "has_sig": false, "md5_digest": "8dbe147182fb01055bb1fa15298826b7", "packagetype": "sdist", "python_version": "source", "requires_python": ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4", "size": 92338, "upload_time": "2019-01-03T23:51:11", "url": "https://files.pythonhosted.org/packages/79/0a/db5df1e02ad1a1ca5b6afbdfe27182ebb832fd1850a454ce6ca1a4fc02ee/dupliganger-0.97.tar.gz" } ], "0.98": [ { "comment_text": "", "digests": { "md5": "fa7a92d07bf6307f054dad4778541f34", "sha256": "55f3ad4ab902483938c9a7cfee759974e9a811c9fafe240754aa3a328b135cc2" }, "downloads": -1, "filename": "dupliganger-0.98.tar.gz", "has_sig": false, "md5_digest": "fa7a92d07bf6307f054dad4778541f34", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 108220, "upload_time": "2019-05-20T23:05:21", "url": "https://files.pythonhosted.org/packages/a4/ab/9cd683d81e5be7ce6a2a3ab9b6c655602116b9096626c3151d04ad313683/dupliganger-0.98.tar.gz" } ] }, "urls": [ { "comment_text": "", "digests": { "md5": "fa7a92d07bf6307f054dad4778541f34", "sha256": "55f3ad4ab902483938c9a7cfee759974e9a811c9fafe240754aa3a328b135cc2" }, "downloads": -1, "filename": "dupliganger-0.98.tar.gz", "has_sig": false, "md5_digest": "fa7a92d07bf6307f054dad4778541f34", "packagetype": "sdist", "python_version": "source", "requires_python": null, "size": 108220, "upload_time": "2019-05-20T23:05:21", "url": "https://files.pythonhosted.org/packages/a4/ab/9cd683d81e5be7ce6a2a3ab9b6c655602116b9096626c3151d04ad313683/dupliganger-0.98.tar.gz" } ] }