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Celine Mercier
2019-12-13 11:28:39 +01:00
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The `OBITools3`: A package for the management of analyses and data in DNA metabarcoding
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### [About the OBITools3](https://git.metabarcoding.org/obitools/obitools3/blob/master/README.md)
### Notes
The OBITools3 are still in beta. They work on OSX and Linux systems, and should work on the Windows Subsystem for Linux soon. If you encounter bugs or want to request a feature, you can do so in [issues](https://git.metabarcoding.org/obitools/obitools3/issues) or by sending an email at <celine.mercier@metabarcoding.org>. You can also see incoming features in the issues.
### Tutorial
* [About the OBITools3](https://git.metabarcoding.org/obitools/obitools3/blob/master/README.md)
Tutorial using most commands:
[Wolf tutorial](Wolf_tutorial)
* [Installing the OBITools3](Installing-the-OBITools3)
### Installing the OBITools3
* [Tutorial using most commands](Wolf-tutorial-with-the-OBITools3)
The OBITools3 are now available to download from git, and will soon be on Nix ([pull request](https://github.com/NixOS/nixpkgs/pull/69644)).
Requirements: **python3, python3-venv, git, CMake**
Then you can do:
git clone https://git.metabarcoding.org/obitools/obitools3.git
cd obitools3
python3 -m venv obi3-env
. obi3-env/bin/activate
pip install cython
python3 setup.py install
. obi_completion_script.sh
And test the installation with:
obi test
### The OBITools3 data structure
* The OBITools3 data structure
The OBITools3 rely on an ad hoc database system, inside which all the data that a DNA metabarcoding experiment must consider is stored: the sequences, the metadata (describing for instance the samples), the database containing the reference sequences used for the taxonomic annotation, as well as the taxonomic databases.