{"id":13442348,"url":"https://github.com/zellerlab/GECCO","last_synced_at":"2025-03-20T13:33:30.139Z","repository":{"id":38364657,"uuid":"328708157","full_name":"zellerlab/GECCO","owner":"zellerlab","description":"GEne Cluster prediction with COnditional random 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align=\"right\" width=\"180\" height=\"180\" src=\"https://raw.githubusercontent.com/zellerlab/GECCO/v0.6.2/static/gecco-square.png\"\u003e\n\n# Hi, I'm GECCO!\n\n## 🦎 ️Overview\n\nGECCO (Gene Cluster prediction with Conditional Random Fields) is a fast and\nscalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs)\nin genomic and metagenomic data using Conditional Random Fields (CRFs).\n\n[![Actions](https://img.shields.io/github/actions/workflow/status/zellerlab/GECCO/test.yml?branch=master\u0026style=flat-square\u0026maxAge=300)](https://github.com/zellerlab/GECCO/actions/workflows/test.yml)\n[![License](https://img.shields.io/badge/license-GPLv3-blue.svg?style=flat-square\u0026maxAge=2678400)](https://choosealicense.com/licenses/gpl-3.0/)\n[![Coverage](https://img.shields.io/codecov/c/gh/zellerlab/GECCO?style=flat-square\u0026maxAge=600)]( https://codecov.io/gh/zellerlab/GECCO/)\n[![Docs](https://img.shields.io/badge/docs-gecco.embl.de-green.svg?maxAge=2678400\u0026style=flat-square)](https://gecco.embl.de)\n[![Source](https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400\u0026style=flat-square)](https://github.com/zellerlab/GECCO/)\n[![Mirror](https://img.shields.io/badge/mirror-EMBL-009f4d?style=flat-square\u0026maxAge=2678400)](https://git.embl.de/grp-zeller/GECCO/)\n[![Changelog](https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400\u0026style=flat-square)](https://github.com/zellerlab/GECCO/blob/master/CHANGELOG.md)\n[![Issues](https://img.shields.io/github/issues/zellerlab/GECCO.svg?style=flat-square\u0026maxAge=600)](https://github.com/zellerlab/GECCO/issues)\n[![Preprint](https://img.shields.io/badge/preprint-bioRxiv-darkblue?style=flat-square\u0026maxAge=2678400)](https://www.biorxiv.org/content/10.1101/2021.05.03.442509v1)\n[![PyPI](https://img.shields.io/pypi/v/gecco-tool.svg?style=flat-square\u0026maxAge=3600)](https://pypi.python.org/pypi/gecco-tool)\n[![Bioconda](https://img.shields.io/conda/vn/bioconda/gecco?style=flat-square\u0026maxAge=3600)](https://anaconda.org/bioconda/gecco)\n[![Galaxy](https://img.shields.io/badge/Galaxy-GECCO-darkblue?style=flat-square\u0026maxAge=3600)](https://toolshed.g2.bx.psu.edu/repository?repository_id=c29bc911b3fc5f8c)\n[![Versions](https://img.shields.io/pypi/pyversions/gecco-tool.svg?style=flat-square\u0026maxAge=3600)](https://pypi.org/project/gecco-tool/#files)\n[![Wheel](https://img.shields.io/pypi/wheel/gecco-tool?style=flat-square\u0026maxAge=3600)](https://pypi.org/project/gecco-tool/#files)\n\n\n## 🔧 Installing GECCO\n\nGECCO is implemented in [Python](https://www.python.org/), and supports [all\nversions](https://endoflife.date/python) from Python 3.7. It requires\nadditional libraries that can be installed directly from\n[PyPI](https://pypi.org), the Python Package Index.\n\nUse [`pip`](https://pip.pypa.io/en/stable/) to install GECCO on your\nmachine:\n```console\n$ pip install gecco-tool\n```\n\nIf you'd rather use [Conda](https://conda.io), a package is available\nin the [`bioconda`](https://bioconda.github.io/) channel. You can install\nwith:\n```console\n$ conda install -c bioconda gecco\n```\n\nThis will install GECCO, its dependencies, and the data needed to run\npredictions. This requires around 40MB of data to be downloaded, so\nit could take some time depending on your Internet connection. Once done,\nyou will have a ``gecco`` command available in your $PATH.\n\n*Note that GECCO uses [HMMER3](http://hmmer.org/), which can only run\non PowerPC and recent x86-64 machines running a POSIX operating system.\nTherefore, GECCO will work on Linux and OSX, but not on Windows.*\n\n\n## 🧬 Running GECCO\n\nOnce `gecco` is installed, you can run it from the terminal by giving it a\nFASTA or GenBank file with the genomic sequence you want to analyze, as\nwell as an output directory:\n\n```console\n$ gecco run --genome some_genome.fna -o some_output_dir\n```\n\nAdditional parameters of interest are:\n\n- `--jobs`, which controls the number of threads that will be spawned by\n  GECCO whenever a step can be parallelized. The default, *0*, will\n  autodetect the number of CPUs on the machine using\n  [`os.cpu_count`](https://docs.python.org/3/library/os.html#os.cpu_count).\n- `--cds`, controlling the minimum number of consecutive genes a BGC region\n  must have to be detected by GECCO. The default is *3*.\n- `--threshold`, controlling the minimum probability for a gene to be\n  considered part of a BGC region. Using a lower number will increase the\n  number (and possibly length) of predictions, but reduce accuracy. The\n  default of *0.8* was selected to optimize precision/recall on a test set\n  of 364 BGCs from [MIBiG 2.0](https://mibig.secondarymetabolites.org/).\n- `--cds-feature`, which can be supplied a feature name to extract genes\n  if the input file already contains gene annotations instead of predicting\n  genes with [Pyrodigal](https://pyrodigal.readthedocs.io). A common value\n  for records downloaded from GenBank is `--cds-feature CDS`.\n\n## 🔎 Results\n\nGECCO will create the following files:\n\n- `{genome}.genes.tsv`: The *genes* file, containing the genes extracted\n  or predicted from the input file, and per-gene BGC probabilities\n  predicted by the CRF.\n- `{genome}.features.tsv`: The *features* file, containing the identified\n  domains in the input sequences, in tabular format.\n- `{genome}.clusters.tsv`: If any were found, a *clusters* file, containing\n  the coordinates of the predicted clusters along their putative biosynthetic\n  type, in tabular format.\n- `{genome}_cluster_{N}.gbk`: If any were found, a GenBank file per cluster,\n  containing the cluster sequence annotated with its member proteins and domains.\n\nGECCO can also convert results to other formats that may be more convenient\ndepending on the downstream usage. GECCO can convert results into:\n\n- GFF3 format so they can be loaded into a genomic viewer \n  (`gecco convert clusters --format gff`).\n- GenBank files with antiSMASH-style features so they can be loaded into \n  [BiG-SLiCE](https://github.com/medema-group/bigslice) for further analysis\n  (`gecco convert gbk --format bigslice`).\n- FASTA files with the sequences of all the predicted BGCs (`gecco convert gbk --format fna`)\n  or with the sequences of all their proteins (`gecco convert gbk --format faa`).\n\nTo get a more visual way of exploring of the predictions, you\ncan open the GenBank files in a genome editing software like [UGENE](http://ugene.net/).\nYou can otherwise load the results into an AntiSMASH report: check the\n[Integrations](https://gecco.embl.de/integrations.html#antismash) page of the\ndocumentation for a step-by-step guide. \n\n\n## 🔖 Reference\n\nGECCO can be cited using the following preprint:\n\n\u003e **Accurate de novo identification of biosynthetic gene clusters with GECCO**.\n\u003e Laura M Carroll, Martin Larralde, Jonas Simon Fleck, Ruby Ponnudurai, Alessio Milanese, Elisa Cappio Barazzone, Georg Zeller.\n\u003e bioRxiv 2021.05.03.442509; [doi:10.1101/2021.05.03.442509](https://doi.org/10.1101/2021.05.03.442509)\n\n\n## 💭 Feedback\n\n### ⚠️ Issue Tracker\n\nFound a bug ? Have an enhancement request ? Head over to the [GitHub issue\ntracker](https://github.com/zellerlab/GECCO/issues) if you need to report\nor ask something. If you are filing in on a bug, please include as much\ninformation as you can about the issue, and try to recreate the same bug\nin a simple, easily reproducible situation.\n\n### 🏗️ Contributing\n\nContributions are more than welcome! See [`CONTRIBUTING.md`](https://github.com/zellerlab/GECCO/blob/master/CONTRIBUTING.md)\nfor more details.\n\n## ⚖️ License\n\nThis software is provided under the [GNU General Public License v3.0 *or later*](https://choosealicense.com/licenses/gpl-3.0/). GECCO is developped by the [Zeller Team](https://www.embl.de/research/units/scb/zeller/index.html)\nat the [European Molecular Biology Laboratory](https://www.embl.de/) in Heidelberg.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzellerlab%2FGECCO","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fzellerlab%2FGECCO","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fzellerlab%2FGECCO/lists"}