{
    "info": {
        "author": "Forest Dussault",
        "author_email": "forest.dussault@canada.ca",
        "bugtrack_url": null,
        "classifiers": [],
        "description": "# ProkaryoteAssembly\n\nTwo simple scripts to assemble prokaryotic genomes using paired-end reads.\n\n## Pipeline Overview\n1. QC on reads with bbduk.sh (adapter trimming/quality filtering)\n2. Error-correction of reads with tadpole.sh\n3. Assembly of reads with skesa\n4. Alignment of error-corrected reads against draft assembly with bbmap.sh\n5. Polishing of assembly with pilon\n\n## Installation\n```\npip install ProkaryoteAssembly\n```\n\n## Usage\nThe first script, `prokaryote_assemble.py`, operates on a single sample at a time.\n\n```\nUsage: prokaryote_assemble.py [OPTIONS]\n\nOptions:\n  -1, --fwd_reads PATH  Path to forward reads (R1) (gzipped FASTQ).\n                        [required]\n  -2, --rev_reads PATH  Path to reverse reads (R2) (gzipped FASTQ).\n                        [required]\n  -o, --out_dir PATH    Root directory to store all output files.  [required]\n  -m, --memory TEXT     Amount of memory to allocate to job. e.g. \"8g\".\n                        Defaults to 8g.\n  --cleanup             Specify this flag to delete all intermediary files\n                        except the resulting FASTA assembly.\n  --version             Specify this flag to print the version and exit.\n  --help                Show this message and exit.\n\n```\n\nThe second script, `prokaryote_assemble_dir.py`, will detect all *.fastq.gz files in\na directory and run the assembly pipeline on each sample it can pair.\n\n```\nUsage: prokaryote_assemble_dir.py [OPTIONS]\n\nOptions:\n  -i, --input_dir PATH  Directory containing all *.fastq.gz files to\n                        assemble.NOTE: Files must be gzipped in order to be\n                        detected.  [required]\n  -o, --out_dir PATH    Root directory to store all output files.  [required]\n  -f, --fwd_id TEXT     Pattern to detect forward reads. Defaults to \"_R1\".\n  -r, --rev_id TEXT     Pattern to detect reverse reads. Defaults to \"_R2\".\n  -m, --memory TEXT     Memory to allocate to pilon call. Defaults to 8g (i.e.\n                        pilon -Xmx8g). May need to provide a large amount of\n                        memory for large read sets/assemblies.\n  --cleanup             Specify this flag to delete all intermediary files\n                        except the resulting FASTA assembly.\n  --version             Specify this flag to print the version and exit.\n  --help                Show this message and exit.\n```\n\n## Python (3.6) Dependencies\n- click\n\n## External Dependencies\n**NOTE:** All external dependencies must be available via PATH.\n\n*Versions confirmed to work are in brackets.*\n- [skesa](https://github.com/ncbi/SKESA) (SKESA v.2.1-SVN_551987:557549M)\n- [BBMap](https://sourceforge.net/projects/bbmap/) (BBMap version 38.22)\n- [samtools](http://www.htslib.org/download/) (samtools 1.8 using htslib 1.8)\n- [pilon](https://github.com/broadinstitute/pilon/wiki) (Pilon version 1.22)\n\n*Note:*\nStrongly recommend installing pilon via conda e.g.\nhttps://bioconda.github.io/recipes/pilon/README.html\n```\nconda install pilon\n```",
        "description_content_type": "text/markdown",
        "docs_url": null,
        "download_url": "",
        "downloads": {
            "last_day": -1,
            "last_month": -1,
            "last_week": -1
        },
        "home_page": "https://github.com/bfssi-forest-dussault/ProkaryoteAssembly",
        "keywords": "",
        "license": "",
        "maintainer": "",
        "maintainer_email": "",
        "name": "ProkaryoteAssembly",
        "package_url": "https://pypi.org/project/ProkaryoteAssembly/",
        "platform": "",
        "project_url": "https://pypi.org/project/ProkaryoteAssembly/",
        "project_urls": {
            "Homepage": "https://github.com/bfssi-forest-dussault/ProkaryoteAssembly"
        },
        "release_url": "https://pypi.org/project/ProkaryoteAssembly/0.1.4/",
        "requires_dist": null,
        "requires_python": "",
        "summary": "Internal BFSSI package for assembling prokaryotic genomes from short reads",
        "version": "0.1.4"
    },
    "last_serial": 5278465,
    "releases": {
        "0.0.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "98ccab622674659effe03cbb2a70ca71",
                    "sha256": "8b24636b6100e5bd8c710afa136dbab52d14fefb3fadaa1c36e3edc74e28c5fd"
                },
                "downloads": -1,
                "filename": "ProkaryoteAssembly-0.0.1-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "98ccab622674659effe03cbb2a70ca71",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 15262,
                "upload_time": "2018-11-15T19:07:28",
                "url": "https://files.pythonhosted.org/packages/9e/77/90730274115c8d1291568cfa7c943e5768042ce9c55e64bc989e2454f26f/ProkaryoteAssembly-0.0.1-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "cb9df00b0a0d2cd586aa2bfae312fd72",
                    "sha256": "44a386af179cb7d5a54502a5213415bbe50f65a96a73ee7510594b45c9d9a3c1"
                },
                "downloads": -1,
                "filename": "ProkaryoteAssembly-0.0.1.tar.gz",
                "has_sig": false,
                "md5_digest": "cb9df00b0a0d2cd586aa2bfae312fd72",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 4991,
                "upload_time": "2018-10-03T12:35:06",
                "url": "https://files.pythonhosted.org/packages/2a/96/31345539d7bd577e654543b7b1badc0f2d1accae97e496311b93bd4e0ea4/ProkaryoteAssembly-0.0.1.tar.gz"
            }
        ],
        "0.0.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "36ecb524a8b8b6cc27bf05c6485497de",
                    "sha256": "9a8d989c46a5a973c9a053af12a090b6ee4a959e2df6ee509693a0b0f099a16e"
                },
                "downloads": -1,
                "filename": "ProkaryoteAssembly-0.0.2-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "36ecb524a8b8b6cc27bf05c6485497de",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 15431,
                "upload_time": "2018-11-15T19:07:29",
                "url": "https://files.pythonhosted.org/packages/08/45/466fd3bd5c176a79456477b32955c938f6225c8e5d50b4d14e8bc1ef5cc9/ProkaryoteAssembly-0.0.2-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "687e9a8526d8f2d0ca5551371e17eefc",
                    "sha256": "a38b4545cabb5c4ce40c3590c96765d92595016a6d6b6525eccc1764873ce959"
                },
                "downloads": -1,
                "filename": "ProkaryoteAssembly-0.0.2.tar.gz",
                "has_sig": false,
                "md5_digest": "687e9a8526d8f2d0ca5551371e17eefc",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 5029,
                "upload_time": "2018-10-03T12:42:38",
                "url": "https://files.pythonhosted.org/packages/0d/c4/c37566f77ee48745b9e82f7b8f38c29838eebb80ac177a934c6695ab3131/ProkaryoteAssembly-0.0.2.tar.gz"
            }
        ],
        "0.0.3": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "c673f4f4566de226ff19184a65ee4e57",
                    "sha256": "ecf34d73533efed1ea1cf9d0e82ae97383458056e14325d7f12c43ec21197f06"
                },
                "downloads": -1,
                "filename": "ProkaryoteAssembly-0.0.3-py3-none-any.whl",
                "has_sig": false,
                "md5_digest": "c673f4f4566de226ff19184a65ee4e57",
                "packagetype": "bdist_wheel",
                "python_version": "py3",
                "requires_python": null,
                "size": 15433,
                "upload_time": "2018-11-15T19:07:31",
                "url": "https://files.pythonhosted.org/packages/85/8d/2bd722882460ba387992f4221aaf19f5c756e3bddad4c52bcf0b44c8565f/ProkaryoteAssembly-0.0.3-py3-none-any.whl"
            },
            {
                "comment_text": "",
                "digests": {
                    "md5": "049dbb9e8e112792b1c318568f6f9b16",
                    "sha256": "d2084536a46b0bc1aa4e002975f4be2e225a7e3396381798ba23d837e73423b5"
                },
                "downloads": -1,
                "filename": "ProkaryoteAssembly-0.0.3.tar.gz",
                "has_sig": false,
                "md5_digest": "049dbb9e8e112792b1c318568f6f9b16",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 5033,
                "upload_time": "2018-10-05T18:32:41",
                "url": "https://files.pythonhosted.org/packages/67/9e/11318b30903b5819a3439391bd7a14dc2c70c1731ec2d4cb050fa37d3615/ProkaryoteAssembly-0.0.3.tar.gz"
            }
        ],
        "0.0.4": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "a84fed53480bf6ae90a95de8e7ea2e41",
                    "sha256": "e495dcbe96ca7c4987f6bbec316efe3267c3c7a522c398b617cc87a5e14667b9"
                },
                "downloads": -1,
                "filename": "ProkaryoteAssembly-0.0.4.tar.gz",
                "has_sig": false,
                "md5_digest": "a84fed53480bf6ae90a95de8e7ea2e41",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 5019,
                "upload_time": "2018-10-05T19:41:37",
                "url": "https://files.pythonhosted.org/packages/5b/e9/d7a10950cc259315149f18cfe566ab687e98c9275c884e550c28157ff2fb/ProkaryoteAssembly-0.0.4.tar.gz"
            }
        ],
        "0.0.5": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "f2f4dbf69812c78532cbc1e6980b3939",
                    "sha256": "239ac77393ebf4fbe84100c81ca9e89d3565a1b3cf7b9291fb94ed68571f653f"
                },
                "downloads": -1,
                "filename": "ProkaryoteAssembly-0.0.5.tar.gz",
                "has_sig": false,
                "md5_digest": "f2f4dbf69812c78532cbc1e6980b3939",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 5033,
                "upload_time": "2018-10-05T19:45:38",
                "url": "https://files.pythonhosted.org/packages/a5/8d/03e830d2b8bfa44e4aa91c8166325e943dc535524941b7ae0923bc3ea8d0/ProkaryoteAssembly-0.0.5.tar.gz"
            }
        ],
        "0.0.6": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "caf00bd59609b7950154fb5e0420fde8",
                    "sha256": "e6dee0807055d3ca190d01a9515569bee6babe2dc1e84a068289f794a9ade536"
                },
                "downloads": -1,
                "filename": "ProkaryoteAssembly-0.0.6.tar.gz",
                "has_sig": false,
                "md5_digest": "caf00bd59609b7950154fb5e0420fde8",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 5032,
                "upload_time": "2018-10-05T19:48:19",
                "url": "https://files.pythonhosted.org/packages/48/76/77384b85b9eae672a792f4f54408bf05b560d7f5522d36bfe753aeda2049/ProkaryoteAssembly-0.0.6.tar.gz"
            }
        ],
        "0.0.7": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "b3a5bcaf42331727b33e3ebada97f3fc",
                    "sha256": "687510dfb5e4b5b8d0d8a72b7367e5c1e92690c38cb8ed094499697a227c9ef8"
                },
                "downloads": -1,
                "filename": "ProkaryoteAssembly-0.0.7.tar.gz",
                "has_sig": false,
                "md5_digest": "b3a5bcaf42331727b33e3ebada97f3fc",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 5141,
                "upload_time": "2018-11-15T19:07:43",
                "url": "https://files.pythonhosted.org/packages/6c/1c/82e3c77f61f7d9f9f01e2112fed5506979dfa03a6818703c52fddaeb457c/ProkaryoteAssembly-0.0.7.tar.gz"
            }
        ],
        "0.0.9": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "d4ade970b51ed5d5ebfe0e2e12b37897",
                    "sha256": "f735d79f6accac892f25dcdd88351e19bc8e63154efe37210b3b2b4464c87105"
                },
                "downloads": -1,
                "filename": "ProkaryoteAssembly-0.0.9.tar.gz",
                "has_sig": false,
                "md5_digest": "d4ade970b51ed5d5ebfe0e2e12b37897",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 5163,
                "upload_time": "2018-11-15T19:16:31",
                "url": "https://files.pythonhosted.org/packages/e8/46/15536406f5240465bf8e5392f251f01457552a1d7bee7f00577ce9ba1a8c/ProkaryoteAssembly-0.0.9.tar.gz"
            }
        ],
        "0.1.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "51fdc708560ec5882346e41046dfb9c6",
                    "sha256": "d9255dbce4a45dd25be26acff70a5d4586477f42105a527c826ed84f46c68698"
                },
                "downloads": -1,
                "filename": "ProkaryoteAssembly-0.1.0.tar.gz",
                "has_sig": false,
                "md5_digest": "51fdc708560ec5882346e41046dfb9c6",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 5163,
                "upload_time": "2018-11-15T19:24:56",
                "url": "https://files.pythonhosted.org/packages/70/6a/57c2f1c5f1bc7d65c804f0815a903f50658379422c423b76fe706085e2ec/ProkaryoteAssembly-0.1.0.tar.gz"
            }
        ],
        "0.1.2": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "fda11ff0a83bea2660e113d6f721df0f",
                    "sha256": "426a8900bbc5eb7051c025de7e382566076b0d92cdf4ae78aa80e96063afe1d4"
                },
                "downloads": -1,
                "filename": "ProkaryoteAssembly-0.1.2.tar.gz",
                "has_sig": false,
                "md5_digest": "fda11ff0a83bea2660e113d6f721df0f",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 5629,
                "upload_time": "2019-04-05T19:03:34",
                "url": "https://files.pythonhosted.org/packages/69/b4/d4a0c4676febd3d80db4e1dbdd77b004ee85ca293fd7741bb280edb182e9/ProkaryoteAssembly-0.1.2.tar.gz"
            }
        ],
        "0.1.3": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "e6184a21d1bf08d48baf1fa40ba818d0",
                    "sha256": "29c03c06818d34deeabea6e5952a8955e488506154554fe2e144a4f82f841dc1"
                },
                "downloads": -1,
                "filename": "ProkaryoteAssembly-0.1.3.tar.gz",
                "has_sig": false,
                "md5_digest": "e6184a21d1bf08d48baf1fa40ba818d0",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 5671,
                "upload_time": "2019-04-05T19:14:37",
                "url": "https://files.pythonhosted.org/packages/83/65/af88b3ae16cdac6b9457e60e21b78827bef1af69de3d1a5346e98c71a34a/ProkaryoteAssembly-0.1.3.tar.gz"
            }
        ],
        "0.1.4": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "f942d5abf240e9ee81845865a0f0b8c6",
                    "sha256": "f791320d772dbc01b75df010575f53863166437d6b3484182b06885684e277da"
                },
                "downloads": -1,
                "filename": "ProkaryoteAssembly-0.1.4.tar.gz",
                "has_sig": false,
                "md5_digest": "f942d5abf240e9ee81845865a0f0b8c6",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 5691,
                "upload_time": "2019-05-16T16:58:01",
                "url": "https://files.pythonhosted.org/packages/95/2f/416940ef86d2813ea28afea5793d0d42cdf37f713a2bad3794920a23a2e4/ProkaryoteAssembly-0.1.4.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "f942d5abf240e9ee81845865a0f0b8c6",
                "sha256": "f791320d772dbc01b75df010575f53863166437d6b3484182b06885684e277da"
            },
            "downloads": -1,
            "filename": "ProkaryoteAssembly-0.1.4.tar.gz",
            "has_sig": false,
            "md5_digest": "f942d5abf240e9ee81845865a0f0b8c6",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": null,
            "size": 5691,
            "upload_time": "2019-05-16T16:58:01",
            "url": "https://files.pythonhosted.org/packages/95/2f/416940ef86d2813ea28afea5793d0d42cdf37f713a2bad3794920a23a2e4/ProkaryoteAssembly-0.1.4.tar.gz"
        }
    ]
}