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57 lines
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57 lines
4.2 KiB
Plaintext
# The OBITools
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The *OBITools4* are programs specifically designed for analyzing NGS data in a DNA metabarcoding context, taking into account taxonomic information. It is distributed as an open source software available on the following website: http://metabarcoding.org/obitools4.
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## Aims of *OBITools*
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DNA metabarcoding is an efficient approach for biodiversity studies [@Taberlet2012-pf]. Originally mainly developed by microbiologists [*e.g.* @Sogin2006-ab], it is now widely used for plants [*e.g.* @Sonstebo2010-vv;@Yoccoz2012-ix;@Parducci2012-rn] and animals from meiofauna [*e.g.* @Chariton2010-cz;@Baldwin2013-yc] to larger organisms [*e.g.* @Andersen2012-gj;@Thomsen2012-au]. Interestingly, this method is not limited to *sensu
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stricto* biodiversity surveys, but it can also be implemented in other
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ecological contexts such as for herbivore [e.g. @Valentini2009-ay;@Kowalczyk2011-kg] or carnivore [e.g. @Deagle2009-yh;@Shehzad2012-pn] diet
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analyses.
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Whatever the biological question under consideration, the DNA metabarcoding
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methodology relies heavily on next-generation sequencing (NGS), and generates
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considerable numbers of DNA sequence reads (typically million of reads).
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Manipulation of such large datasets requires dedicated programs usually running
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on a Unix system. Unix is an operating system, whose first version was created
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during the sixties. Since its early stages, it is dedicated to scientific
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computing and includes a large set of simple tools to efficiently process text
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files. Most of those programs can be viewed as filters extracting information
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from a text file to create a new text file. These programs process text files as
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streams, line per line, therefore allowing computation on a huge dataset without
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requiring a large memory. Unix programs usually print their results to their
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standard output (*stdout*), which by default is the terminal, so the results can
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be examined on screen. The main philosophy of the Unix environment is to allow
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easy redirection of the *stdout* either to a file, for saving the results, or to
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the standard input (*stdin*) of a second program thus allowing to easily create
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complex processing from simple base commands. Access to Unix computers is
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increasingly easier for scientists nowadays. Indeed, the Linux operating system,
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an open source version of Unix, can be freely installed on every PC machine and
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the MacOS operating system, running on Apple computers, is also a Unix system.
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The *OBITools* programs imitate Unix standard programs because they usually act as
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filters, reading their data from text files or the *stdin* and writing their
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results to the *stdout*. The main difference with classical Unix programs is that
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text files are not analyzed line per line but sequence record per sequence
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record (see below for a detailed description of a sequence record).
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Compared to packages for similar purposes like mothur [@Schloss2009-qy] or
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QIIME [@Caporaso2010-ii], the *OBITools* mainly rely on filtering and sorting
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algorithms. This allows users to set up versatile data analysis pipelines
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(Figure 1), adjustable to the broad range of DNA metabarcoding applications.
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The innovation of the *OBITools* is their ability to take into account the
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taxonomic annotations, ultimately allowing sorting and filtering of sequence
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records based on the taxonomy.
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## Installation of the obitools
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### Availability of the OBITools
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The *OBITools* are open source and protected by the [CeCILL 2.1 license](http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html).
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All the sources of the [*OBITools4*](http://metabarcoding.org/obitools4) can be downloaded from the metabarcoding git server (https://git.metabarcoding.org).
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### Prerequisites
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The *OBITools4* are developped using the [GO programming language](https://go.dev/), we stick to the latest version of the language, today the $1.19.5$. If you want to download and compile the sources yourself, you first need to install the corresponding compiler on your system. Some parts of the soft are also written in C, therefore a recent C compiler is also requested, GCC on Linux or Windows, the Developer Tools on Mac.
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Whatever the installation you decide for, you will have to ensure that a C compiler is available on your system. |