obitools4/doc/book/intro.qmd

# The OBITools

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.


## Aims of *OBITools*

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
stricto* biodiversity surveys, but it can also be implemented in other
ecological contexts such as for herbivore [e.g. @Valentini2009-ay;@Kowalczyk2011-kg] or carnivore [e.g. @Deagle2009-yh;@Shehzad2012-pn] diet
analyses.

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 (*stdout*), 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 *stdout* either to a file, for saving the results, or to
the standard input (*stdin*) 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 *OBITools* programs imitate Unix standard programs because they usually act as
filters, reading their data from text files or the *stdin* and writing their
results to the *stdout*. 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 [@Schloss2009-qy] or
QIIME [@Caporaso2010-ii], the *OBITools* 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 *OBITools* is their ability to take into account the
taxonomic annotations, ultimately allowing sorting and filtering of sequence
records based on the taxonomy.