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1 Hi, I’m GECCO!
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2 ==============
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3
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4 .. image:: https://raw.githubusercontent.com/zellerlab/GECCO/v0.6.2/static/gecco-square.png
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5 :target: https://github.com/zellerlab/GECCO/
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6
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7
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8 🦎 ️Overview
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9 ---------------
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10
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11 GECCO (Gene Cluster prediction with Conditional Random Fields) is a fast
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12 and scalable method for identifying putative novel Biosynthetic Gene
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13 Clusters (BGCs) in genomic and metagenomic data using Conditional Random
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14 Fields (CRFs).
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15
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16 |GitLabCI| |License| |Coverage| |Docs| |Source| |Mirror| |Changelog|
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17 |Issues| |Preprint| |PyPI| |Bioconda| |Versions| |Wheel|
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18
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19 🔧 Installing GECCO
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20 -------------------
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21
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22 GECCO is implemented in `Python <https://www.python.org/>`__, and
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23 supports `all versions <https://endoflife.date/python>`__ from Python
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24 3.6. It requires additional libraries that can be installed directly
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25 from `PyPI <https://pypi.org>`__, the Python Package Index.
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26
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27 Use `pip <https://pip.pypa.io/en/stable/>`__ to install GECCO on
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28 your machine::
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29
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30 $ pip install gecco-tool
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31
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32 If you’d rather use `Conda <https://conda.io>`__, a package is available
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33 in the `bioconda <https://bioconda.github.io/>`__ channel. You can
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34 install with::
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35
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36 $ conda install -c bioconda gecco
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37
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38 This will install GECCO, its dependencies, and the data needed to run
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39 predictions. This requires around 100MB of data to be downloaded, so it
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40 could take some time depending on your Internet connection. Once done,
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41 you will have a ``gecco`` command available in your $PATH.
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42
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43 *Note that GECCO uses* `HMMER3 <http://hmmer.org/>`__, *which can
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44 only run on PowerPC and recent x86-64 machines running a POSIX operating
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45 system. Therefore, Linux and OSX are supported platforms, but GECCO will
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46 not be able to run on Windows.*
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47
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48 🧬 Running GECCO
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49 -----------------
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50
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51 Once ``gecco`` is installed, you can run it from the terminal by giving
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52 it a FASTA or GenBank file with the genomic sequence you want to
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53 analyze, as well as an output directory::
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54
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55 $ gecco run --genome some_genome.fna -o some_output_dir
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56
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57 Additional parameters of interest are:
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58
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59 - ``--jobs``, which controls the number of threads that will be spawned
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60 by GECCO whenever a step can be parallelized. The default, *0*, will
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61 autodetect the number of CPUs on the machine using
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62 `os.cpu_count <https://docs.python.org/3/library/os.html#os.cpu_count>`__.
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63 - ``--cds``, controlling the minimum number of consecutive genes a BGC
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64 region must have to be detected by GECCO (default is 3).
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65 - ``--threshold``, controlling the minimum probability for a gene to be
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66 considered part of a BGC region. Using a lower number will increase
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67 the number (and possibly length) of predictions, but reduce accuracy.
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68
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69 🔖 Reference
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70 -------------
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71
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72 GECCO can be cited using the following preprint:
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73
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74 **Accurate de novo identification of biosynthetic gene clusters with
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75 GECCO**. Laura M Carroll, Martin Larralde, Jonas Simon Fleck, Ruby
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76 Ponnudurai, Alessio Milanese, Elisa Cappio Barazzone, Georg Zeller.
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77 bioRxiv 2021.05.03.442509;
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78 `doi:10.1101/2021.05.03.442509 <https://doi.org/10.1101/2021.05.03.442509>`__
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79
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80 💭 Feedback
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81 ------------
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82
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83 ⚠️ Issue Tracker
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84 ~~~~~~~~~~~~~~~~
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85
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86 Found a bug ? Have an enhancement request ? Head over to the `GitHub
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87 issue tracker <https://github.com/zellerlab/GECCO/issues>`__ if you need
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88 to report or ask something. If you are filing in on a bug, please
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89 include as much information as you can about the issue, and try to
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90 recreate the same bug in a simple, easily reproducible situation.
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91
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92 🏗️ Contributing
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93 ~~~~~~~~~~~~~~~~
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94
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95 Contributions are more than welcome! See
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96 `CONTRIBUTING.md <https://github.com/althonos/pyhmmer/blob/master/CONTRIBUTING.md>`__
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97 for more details.
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98
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99 ⚖️ License
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100 ----------
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101
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102 This software is provided under the `GNU General Public License v3.0 or
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103 later <https://choosealicense.com/licenses/gpl-3.0/>`__. GECCO is
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104 developped by the `Zeller
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105 Team <https://www.embl.de/research/units/scb/zeller/index.html>`__ at
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106 the `European Molecular Biology Laboratory <https://www.embl.de/>`__ in
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107 Heidelberg.
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108
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109 .. |GitLabCI| image:: https://img.shields.io/gitlab/pipeline/grp-zeller/GECCO/master?gitlab_url=https%3A%2F%2Fgit.embl.de&style=flat-square&maxAge=600
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110 :target: https://git.embl.de/grp-zeller/GECCO/-/pipelines/
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111 .. |License| image:: https://img.shields.io/badge/license-GPLv3-blue.svg?style=flat-square&maxAge=2678400
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112 :target: https://choosealicense.com/licenses/gpl-3.0/
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113 .. |Coverage| image:: https://img.shields.io/codecov/c/gh/zellerlab/GECCO?style=flat-square&maxAge=600
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114 :target: https://codecov.io/gh/zellerlab/GECCO/
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115 .. |Docs| image:: https://img.shields.io/badge/docs-gecco.embl.de-green.svg?maxAge=2678400&style=flat-square
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116 :target: https://gecco.embl.de
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117 .. |Source| image:: https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square
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118 :target: https://github.com/zellerlab/GECCO/
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119 .. |Mirror| image:: https://img.shields.io/badge/mirror-EMBL-009f4d?style=flat-square&maxAge=2678400
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120 :target: https://git.embl.de/grp-zeller/GECCO/
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121 .. |Changelog| image:: https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square
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122 :target: https://github.com/zellerlab/GECCO/blob/master/CHANGELOG.md
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123 .. |Issues| image:: https://img.shields.io/github/issues/zellerlab/GECCO.svg?style=flat-square&maxAge=600
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124 :target: https://github.com/zellerlab/GECCO/issues
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125 .. |Preprint| image:: https://img.shields.io/badge/preprint-bioRxiv-darkblue?style=flat-square&maxAge=2678400
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126 :target: https://www.biorxiv.org/content/10.1101/2021.05.03.442509v1
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127 .. |PyPI| image:: https://img.shields.io/pypi/v/gecco-tool.svg?style=flat-square&maxAge=3600
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128 :target: https://pypi.python.org/pypi/gecco-tool
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129 .. |Bioconda| image:: https://img.shields.io/conda/vn/bioconda/gecco?style=flat-square&maxAge=3600
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130 :target: https://anaconda.org/bioconda/gecco
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131 .. |Versions| image:: https://img.shields.io/pypi/pyversions/gecco-tool.svg?style=flat-square&maxAge=3600
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132 :target: https://pypi.org/project/gecco-tool/#files
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133 .. |Wheel| image:: https://img.shields.io/pypi/wheel/gecco-tool?style=flat-square&maxAge=3600
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134 :target: https://pypi.org/project/gecco-tool/#files
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