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"Release v0.8.4"
author althonos
date Sun, 21 Nov 2021 16:53:12 +0000
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1 Hi, I’m GECCO!
2 ==============
3
4 🦎 ️Overview
5 ---------------
6
7 GECCO (Gene Cluster prediction with Conditional Random Fields) is a fast
8 and scalable method for identifying putative novel Biosynthetic Gene
9 Clusters (BGCs) in genomic and metagenomic data using Conditional Random
10 Fields (CRFs).
11
12 |GitLabCI| |License| |Coverage| |Docs| |Source| |Mirror| |Changelog|
13 |Issues| |Preprint| |PyPI| |Bioconda| |Versions| |Wheel|
14
15 🔧 Installing GECCO
16 -------------------
17
18 GECCO is implemented in `Python <https://www.python.org/>`__, and
19 supports `all versions <https://endoflife.date/python>`__ from Python
20 3.6. It requires additional libraries that can be installed directly
21 from `PyPI <https://pypi.org>`__, the Python Package Index.
22
23 Use ```pip`` <https://pip.pypa.io/en/stable/>`__ to install GECCO on
24 your machine:
25
26 .. code:: console
27
28 $ pip install gecco-tool
29
30 If you’d rather use `Conda <https://conda.io>`__, a package is available
31 in the ```bioconda`` <https://bioconda.github.io/>`__ channel. You can
32 install with:
33
34 .. code:: console
35
36 $ conda install -c bioconda gecco
37
38 This will install GECCO, its dependencies, and the data needed to run
39 predictions. This requires around 100MB of data to be downloaded, so it
40 could take some time depending on your Internet connection. Once done,
41 you will have a ``gecco`` command available in your $PATH.
42
43 *Note that GECCO uses*\ `HMMER3 <http://hmmer.org/>`__\ *, which can
44 only run on PowerPC and recent x86-64 machines running a POSIX operating
45 system. Therefore, Linux and OSX are supported platforms, but GECCO will
46 not be able to run on Windows.*
47
48 🧬 Running GECCO
49 -----------------
50
51 Once ``gecco`` is installed, you can run it from the terminal by giving
52 it a FASTA or GenBank file with the genomic sequence you want to
53 analyze, as well as an output directory:
54
55 .. code:: console
56
57 $ gecco run --genome some_genome.fna -o some_output_dir
58
59 Additional parameters of interest are:
60
61 - ``--jobs``, which controls the number of threads that will be spawned
62 by GECCO whenever a step can be parallelized. The default, *0*, will
63 autodetect the number of CPUs on the machine using
64 ```os.cpu_count`` <https://docs.python.org/3/library/os.html#os.cpu_count>`__.
65 - ``--cds``, controlling the minimum number of consecutive genes a BGC
66 region must have to be detected by GECCO (default is 3).
67 - ``--threshold``, controlling the minimum probability for a gene to be
68 considered part of a BGC region. Using a lower number will increase
69 the number (and possibly length) of predictions, but reduce accuracy.
70
71 🔖 Reference
72 -------------
73
74 GECCO can be cited using the following preprint:
75
76 **Accurate de novo identification of biosynthetic gene clusters with
77 GECCO**. Laura M Carroll, Martin Larralde, Jonas Simon Fleck, Ruby
78 Ponnudurai, Alessio Milanese, Elisa Cappio Barazzone, Georg Zeller.
79 bioRxiv 2021.05.03.442509;
80 `doi:10.1101/2021.05.03.442509 <https://doi.org/10.1101/2021.05.03.442509>`__
81
82 💭 Feedback
83 ------------
84
85 ⚠️ Issue Tracker
86 ~~~~~~~~~~~~~~~~
87
88 Found a bug ? Have an enhancement request ? Head over to the `GitHub
89 issue tracker <https://github.com/zellerlab/GECCO/issues>`__ if you need
90 to report or ask something. If you are filing in on a bug, please
91 include as much information as you can about the issue, and try to
92 recreate the same bug in a simple, easily reproducible situation.
93
94 🏗️ Contributing
95 ~~~~~~~~~~~~~~~~
96
97 Contributions are more than welcome! See
98 ```CONTRIBUTING.md`` <https://github.com/althonos/pyhmmer/blob/master/CONTRIBUTING.md>`__
99 for more details.
100
101 ⚖️ License
102 ----------
103
104 This software is provided under the `GNU General Public License v3.0 or
105 later <https://choosealicense.com/licenses/gpl-3.0/>`__. GECCO is
106 developped by the `Zeller
107 Team <https://www.embl.de/research/units/scb/zeller/index.html>`__ at
108 the `European Molecular Biology Laboratory <https://www.embl.de/>`__ in
109 Heidelberg.
110
111 .. |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
112 :target: https://git.embl.de/grp-zeller/GECCO/-/pipelines/
113 .. |License| image:: https://img.shields.io/badge/license-GPLv3-blue.svg?style=flat-square&maxAge=2678400
114 :target: https://choosealicense.com/licenses/gpl-3.0/
115 .. |Coverage| image:: https://img.shields.io/codecov/c/gh/zellerlab/GECCO?style=flat-square&maxAge=600
116 :target: https://codecov.io/gh/zellerlab/GECCO/
117 .. |Docs| image:: https://img.shields.io/badge/docs-gecco.embl.de-green.svg?maxAge=2678400&style=flat-square
118 :target: https://gecco.embl.de
119 .. |Source| image:: https://img.shields.io/badge/source-GitHub-303030.svg?maxAge=2678400&style=flat-square
120 :target: https://github.com/zellerlab/GECCO/
121 .. |Mirror| image:: https://img.shields.io/badge/mirror-EMBL-009f4d?style=flat-square&maxAge=2678400
122 :target: https://git.embl.de/grp-zeller/GECCO/
123 .. |Changelog| image:: https://img.shields.io/badge/keep%20a-changelog-8A0707.svg?maxAge=2678400&style=flat-square
124 :target: https://github.com/zellerlab/GECCO/blob/master/CHANGELOG.md
125 .. |Issues| image:: https://img.shields.io/github/issues/zellerlab/GECCO.svg?style=flat-square&maxAge=600
126 :target: https://github.com/zellerlab/GECCO/issues
127 .. |Preprint| image:: https://img.shields.io/badge/preprint-bioRxiv-darkblue?style=flat-square&maxAge=2678400
128 :target: https://www.biorxiv.org/content/10.1101/2021.05.03.442509v1
129 .. |PyPI| image:: https://img.shields.io/pypi/v/gecco-tool.svg?style=flat-square&maxAge=3600
130 :target: https://pypi.python.org/pypi/gecco-tool
131 .. |Bioconda| image:: https://img.shields.io/conda/vn/bioconda/gecco?style=flat-square&maxAge=3600
132 :target: https://anaconda.org/bioconda/gecco
133 .. |Versions| image:: https://img.shields.io/pypi/pyversions/gecco-tool.svg?style=flat-square&maxAge=3600
134 :target: https://pypi.org/project/gecco-tool/#files
135 .. |Wheel| image:: https://img.shields.io/pypi/wheel/gecco-tool?style=flat-square&maxAge=3600
136 :target: https://pypi.org/project/gecco-tool/#files