<ahref="./library.html"class="sidebar-item-text sidebar-link"><spanclass="chapter-number">5</span> <spanclass="chapter-title">The GO <em>OBITools</em> library</span></a>
<li><ahref="#aims-of-obitools"id="toc-aims-of-obitools"class="nav-link active"data-scroll-target="#aims-of-obitools"><spanclass="toc-section-number">1.1</span> Aims of <em>OBITools</em></a></li>
<li><ahref="#installation-of-the-obitools"id="toc-installation-of-the-obitools"class="nav-link"data-scroll-target="#installation-of-the-obitools"><spanclass="toc-section-number">1.2</span> Installation of the obitools</a>
<li><ahref="#availability-of-the-obitools"id="toc-availability-of-the-obitools"class="nav-link"data-scroll-target="#availability-of-the-obitools"><spanclass="toc-section-number">1.2.1</span> Availability of the OBITools</a></li>
<p>The <em>OBITools4</em> 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.</p>
<p>DNA metabarcoding is an efficient approach for biodiversity studies <spanclass="citation"data-cites="Taberlet2012-pf">(<ahref="references.html#ref-Taberlet2012-pf"role="doc-biblioref">Taberlet et al. 2012</a>)</span>. Originally mainly developed by microbiologists <spanclass="citation"data-cites="Sogin2006-ab">(<em>e.g.</em><ahref="references.html#ref-Sogin2006-ab"role="doc-biblioref">Sogin et al. 2006</a>)</span>, it is now widely used for plants <spanclass="citation"data-cites="Sonstebo2010-vv Yoccoz2012-ix Parducci2012-rn">(<em>e.g.</em><ahref="references.html#ref-Sonstebo2010-vv"role="doc-biblioref">Sønstebø et al. 2010</a>; <ahref="references.html#ref-Yoccoz2012-ix"role="doc-biblioref">Yoccoz et al. 2012</a>; <ahref="references.html#ref-Parducci2012-rn"role="doc-biblioref">Parducci et al. 2012</a>)</span> and animals from meiofauna <spanclass="citation"data-cites="Chariton2010-cz Baldwin2013-yc">(<em>e.g.</em><ahref="references.html#ref-Chariton2010-cz"role="doc-biblioref">Chariton et al. 2010</a>; <ahref="references.html#ref-Baldwin2013-yc"role="doc-biblioref">Baldwin et al. 2013</a>)</span> to larger organisms <spanclass="citation"data-cites="Andersen2012-gj Thomsen2012-au">(<em>e.g.</em><ahref="references.html#ref-Andersen2012-gj"role="doc-biblioref">Andersen et al. 2012</a>; <ahref="references.html#ref-Thomsen2012-au"role="doc-biblioref">Thomsen et al. 2012</a>)</span>. Interestingly, this method is not limited to <em>sensu stricto</em> biodiversity surveys, but it can also be implemented in other ecological contexts such as for herbivore <spanclass="citation"data-cites="Valentini2009-ay Kowalczyk2011-kg">(e.g. <ahref="references.html#ref-Valentini2009-ay"role="doc-biblioref">Valentini et al. 2009</a>; <ahref="references.html#ref-Kowalczyk2011-kg"role="doc-biblioref">Kowalczyk et al. 2011</a>)</span> or carnivore <spanclass="citation"data-cites="Deagle2009-yh Shehzad2012-pn">(e.g. <ahref="references.html#ref-Deagle2009-yh"role="doc-biblioref">Deagle, Kirkwood, and Jarman 2009</a>; <ahref="references.html#ref-Shehzad2012-pn"role="doc-biblioref">Shehzad et al. 2012</a>)</span> diet analyses.</p>
<p>Whatever the biological question under consideration, the DNA metabarcoding methodology relies heavily on next-generation sequencing (NGS), and generates considerable numbers of DNA sequence reads (typically million of reads). Manipulation of such large datasets requires dedicated programs usually running on a Unix system. Unix is an operating system, whose first version was created during the sixties. Since its early stages, it is dedicated to scientific computing and includes a large set of simple tools to efficiently process text files. Most of those programs can be viewed as filters extracting information from a text file to create a new text file. These programs process text files as streams, line per line, therefore allowing computation on a huge dataset without requiring a large memory. Unix programs usually print their results to their standard output (<em>stdout</em>), which by default is the terminal, so the results can be examined on screen. The main philosophy of the Unix environment is to allow easy redirection of the <em>stdout</em> either to a file, for saving the results, or to the standard input (<em>stdin</em>) of a second program thus allowing to easily create complex processing from simple base commands. Access to Unix computers is increasingly easier for scientists nowadays. Indeed, the Linux operating system, an open source version of Unix, can be freely installed on every PC machine and the MacOS operating system, running on Apple computers, is also a Unix system. The <em>OBITools</em> programs imitate Unix standard programs because they usually act as filters, reading their data from text files or the <em>stdin</em> and writing their results to the <em>stdout</em>. The main difference with classical Unix programs is that text files are not analyzed line per line but sequence record per sequence record (see below for a detailed description of a sequence record). Compared to packages for similar purposes like mothur <spanclass="citation"data-cites="Schloss2009-qy">(<ahref="references.html#ref-Schloss2009-qy"role="doc-biblioref">Schloss et al. 2009</a>)</span> or QIIME <spanclass="citation"data-cites="Caporaso2010-ii">(<ahref="references.html#ref-Caporaso2010-ii"role="doc-biblioref">Caporaso et al. 2010</a>)</span>, the <em>OBITools</em> mainly rely on filtering and sorting algorithms. This allows users to set up versatile data analysis pipelines (Figure 1), adjustable to the broad range of DNA metabarcoding applications. The innovation of the <em>OBITools</em> is their ability to take into account the taxonomic annotations, ultimately allowing sorting and filtering of sequence records based on the taxonomy.</p>
<h2data-number="1.2"class="anchored"data-anchor-id="installation-of-the-obitools"><spanclass="header-section-number">1.2</span> Installation of the obitools</h2>
<h3data-number="1.2.1"class="anchored"data-anchor-id="availability-of-the-obitools"><spanclass="header-section-number">1.2.1</span> Availability of the OBITools</h3>
<p>The <em>OBITools</em> are open source and protected by the <ahref="http://www.cecill.info/licences/Licence_CeCILL_V2.1-en.html">CeCILL 2.1 license</a>.</p>
<p>All the sources of the <ahref="http://metabarcoding.org/obitools4"><em>OBITools4</em></a> can be downloaded from the metabarcoding git server (https://git.metabarcoding.org).</p>
<p>The <em>OBITools4</em> are developped using the <ahref="https://go.dev/">GO programming language</a>, we stick to the latest version of the language, today the <spanclass="math inline">\(1.19.5\)</span>. 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.</p>
<p>Whatever the installation you decide for, you will have to ensure that a C compiler is available on your system.</p>
Andersen, Kenneth, Karen Lise Bird, Morten Rasmussen, James Haile, Henrik Breuning-Madsen, Kurt H Kjaer, Ludovic Orlando, M Thomas P Gilbert, and Eske Willerslev. 2012. <span>“<spanclass="nocase">Meta-barcoding of <spanclass="nocase">ë</span>dirt<spanclass="nocase">ı́</span>DNA from soil reflects vertebrate biodiversity</span>.”</span><em>Molecular Ecology</em> 21 (8): 1966–79.
Baldwin, Darren S, Matthew J Colloff, Gavin N Rees, Anthony A Chariton, Garth O Watson, Leon N Court, Diana M Hartley, et al. 2013. <span>“<spanclass="nocase">Impacts of inundation and drought on eukaryote biodiversity in semi-arid floodplain soils</span>.”</span><em>Molecular Ecology</em> 22 (6): 1746–58. <ahref="https://doi.org/10.1111/mec.12190">https://doi.org/10.1111/mec.12190</a>.
Chariton, Anthony A, Anthony C Roach, Stuart L Simpson, and Graeme E Batley. 2010. <span>“<spanclass="nocase">Influence of the choice of physical and chemistry variables on interpreting patterns of sediment contaminants and their relationships with estuarine macrobenthic communities</span>.”</span><em>Marine and Freshwater Research</em>. <ahref="https://doi.org/10.1071/mf09263">https://doi.org/10.1071/mf09263</a>.
Deagle, Bruce E, Roger Kirkwood, and Simon N Jarman. 2009. <span>“<spanclass="nocase">Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces</span>.”</span><em>Molecular Ecology</em> 18 (9): 2022–38. <ahref="https://doi.org/10.1111/j.1365-294X.2009.04158.x">https://doi.org/10.1111/j.1365-294X.2009.04158.x</a>.
Kowalczyk, Rafał, Pierre Taberlet, Eric Coissac, Alice Valentini, Christian Miquel, Tomasz Kamiński, and Jan M Wójcik. 2011. <span>“<spanclass="nocase">Influence of management practices on large herbivore diet—Case of European bison in Bia<spanclass="nocase">ł</span>owie<spanclass="nocase">ż</span>a Primeval Forest (Poland)</span>.”</span><em>Forest Ecology and Management</em> 261 (4): 821–28. <ahref="https://doi.org/10.1016/j.foreco.2010.11.026">https://doi.org/10.1016/j.foreco.2010.11.026</a>.
Parducci, Laura, Tina Jørgensen, Mari Mette Tollefsrud, Ellen Elverland, Torbjørn Alm, Sonia L Fontana, K D Bennett, et al. 2012. <span>“<spanclass="nocase">Glacial survival of boreal trees in northern Scandinavia</span>.”</span><em>Science</em> 335 (6072): 1083–86. <ahref="https://doi.org/10.1126/science.1216043">https://doi.org/10.1126/science.1216043</a>.
Schloss, Patrick D, Sarah L Westcott, Thomas Ryabin, Justine R Hall, Martin Hartmann, Emily B Hollister, Ryan A Lesniewski, et al. 2009. <span>“<spanclass="nocase">Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities</span>.”</span><em>Applied and Environmental Microbiology</em> 75 (23): 7537–41. <ahref="https://doi.org/10.1128/AEM.01541-09">https://doi.org/10.1128/AEM.01541-09</a>.
Shehzad, Wasim, Tiayyba Riaz, Muhammad A Nawaz, Christian Miquel, Carole Poillot, Safdar A Shah, Francois Pompanon, Eric Coissac, and Pierre Taberlet. 2012. <span>“<spanclass="nocase">Carnivore diet analysis based on next-generation sequencing: Application to the leopard cat (Prionailurus bengalensis) in Pakistan</span>.”</span><em>Molecular Ecology</em> 21 (8): 1951–65. <ahref="https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2011.05424.x">https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1365-294X.2011.05424.x</a>.
Sogin, Mitchell L, Hilary G Morrison, Julie A Huber, David Mark Welch, Susan M Huse, Phillip R Neal, Jesus M Arrieta, and Gerhard J Herndl. 2006. <span>“<spanclass="nocase">Microbial diversity in the deep sea and the underexplored "rare biosphere"</span>.”</span><em>Proceedings of the National Academy of Sciences of the United States of America</em> 103 (32): 12115–20. <ahref="https://doi.org/10.1073/pnas.0605127103">https://doi.org/10.1073/pnas.0605127103</a>.
Sønstebø, J H, L Gielly, A K Brysting, R Elven, M Edwards, J Haile, E Willerslev, et al. 2010. <span>“<spanclass="nocase">Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate</span>.”</span><em>Molecular Ecology Resources</em> 10 (6): 1009–18. <ahref="https://doi.org/10.1111/j.1755-0998.2010.02855.x">https://doi.org/10.1111/j.1755-0998.2010.02855.x</a>.
Thomsen, Philip Francis, Jos Kielgast, Lars L Iversen, Carsten Wiuf, Morten Rasmussen, M Thomas P Gilbert, Ludovic Orlando, and Eske Willerslev. 2012. <span>“<spanclass="nocase">Monitoring endangered freshwater biodiversity using environmental DNA</span>.”</span><em>Molecular Ecology</em> 21 (11): 2565–73. <ahref="https://doi.org/10.1111/j.1365-294X.2011.05418.x">https://doi.org/10.1111/j.1365-294X.2011.05418.x</a>.
Valentini, Alice, Christian Miquel, Muhammad Ali Nawaz, Eva Bellemain, Eric Coissac, François Pompanon, Ludovic Gielly, et al. 2009. <span>“<spanclass="nocase">New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: the trnL approach</span>.”</span><em>Molecular Ecology Resources</em> 9 (1): 51–60. <ahref="https://doi.org/10.1111/j.1755-0998.2008.02352.x">https://doi.org/10.1111/j.1755-0998.2008.02352.x</a>.
Yoccoz, N G, K A Bråthen, L Gielly, J Haile, M E Edwards, T Goslar, H Von Stedingk, et al. 2012. <span>“<spanclass="nocase">DNA from soil mirrors plant taxonomic and growth form diversity</span>.”</span><em>Molecular Ecology</em> 21 (15): 3647–55. <ahref="https://doi.org/10.1111/j.1365-294X.2012.05545.x">https://doi.org/10.1111/j.1365-294X.2012.05545.x</a>.
