home.markdown

-= OBITools =
+OBITools
+========
 
-
-'''OBITools''' is a set of python programs developed to simplify the manipulation of sequence files in our labs. 
-They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) 
-in the context of [http://metabarcoding.org DNA Metabarcoding]. 
+**OBITools** is a set of python programs developed to simplify the manipulation of sequence files in our labs. They were mainly designed to help us for analyzing Next Generation Sequencer outputs (454 or Illumina) in the context of [DNA Metabarcoding](http://metabarcoding.org).
 
 They are highly related with the following softwares:
 
-     - [http://www.grenoble.prabi.fr/trac/ecoPCR ecoPCR] for [http://metabarcoding.org DNA Metabarcoding] primers in silico evaluation.
-     - [http://www.grenoble.prabi.fr/trac/ecoPrimers ecoPrimers] for [http://metabarcoding.org DNA Metabarcoding] primers design.
-     - [http://metabarcoding.org/sumatra sumatra and sumaclust] for fast alignment and clustering of NGS reads.
-
-The programs evolved with our needs. They mainly provide facilities to manipulate sequence files in [http://en.wikipedia.org/wiki/FASTA_format Fasta] and 
-[http://en.wikipedia.org/wiki/FASTQ_format FastQ] format. Other input formats like [http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html genbank] 
-or [http://en.wikipedia.org/wiki/European_Nucleotide_Archive embl] are supported too as well as formats related to 
-[http://www.grenoble.prabi.fr/trac/ecoPCR ecoPCR]. 
+`    - `[`ecoPCR`](http://www.grenoble.prabi.fr/trac/ecoPCR)` for `[`DNA` `Metabarcoding`](http://metabarcoding.org)` primers in silico evaluation.`
+`    - `[`ecoPrimers`](http://www.grenoble.prabi.fr/trac/ecoPrimers)` for `[`DNA` `Metabarcoding`](http://metabarcoding.org)` primers design.`
+`    - `[`sumatra` `and` `sumaclust`](http://metabarcoding.org/sumatra)` for fast alignment and clustering of NGS reads.`
 
-== The '''OBITools''' programs ==
+The programs evolved with our needs. They mainly provide facilities to manipulate sequence files in [Fasta](http://en.wikipedia.org/wiki/FASTA_format) and [FastQ](http://en.wikipedia.org/wiki/FASTQ_format) format. Other input formats like [genbank](http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html) or [embl](http://en.wikipedia.org/wiki/European_Nucleotide_Archive) are supported too as well as formats related to [ecoPCR](http://www.grenoble.prabi.fr/trac/ecoPCR).
 
-The '''OBITools''' programs aims to help you to manipulate various data and sequence files in a convenient way using the
-''Unix'' command line interface.
-They follow the standard ''Unix'' interface for command line program, allowing to chain a set of commands
-using the pipe mecanism. 
+The **OBITools** programs
+-------------------------
 
-All these programs have a {{{-h}}} option printing a small online help to describe the different options accepted by the programs.
-A complete documentation is available [http://metabarcoding.org/obitools/doc here]
+The **OBITools** programs aims to help you to manipulate various data and sequence files in a convenient way using the *Unix* command line interface. They follow the standard *Unix* interface for command line program, allowing to chain a set of commands using the pipe mecanism.
 
-Most of the  '''OBITools''' programs' names start by `obi`. By using the command autocompletion behavior of your unix shell you
-can have easily access to all the command name.
+All these programs have a option printing a small online help to describe the different options accepted by the programs. A complete documentation is available [here](http://metabarcoding.org/obitools/doc)
 
+Most of the **OBITools** programs' names start by \`obi\`. By using the command autocompletion behavior of your unix shell you can have easily access to all the command name.
 
-== Some way to use '''obitools''' == 
+Some way to use **obitools**
+----------------------------
 
-A complete tutorial, demonstrating how to analyse DNA metabarcoding data using '''OBITools''' is available [http://metabarcoding.org/obitools/doc here]
+A complete tutorial, demonstrating how to analyse DNA metabarcoding data using **OBITools** is available [here](http://metabarcoding.org/obitools/doc)
 
-== Download and install '''OBITools''' ==
+Download and install **OBITools**
+---------------------------------
 
-OBITools are deposed on the PYPI archive site, you can easily install them on your computer using the Python 
-[http://pip.readthedocs.org/en/latest/installing.html pip] installer. We recommend the [http://pip.readthedocs.org/en/latest/installing.html pip]
-installer rather than the `easy_install` one as [http://pip.readthedocs.org/en/latest/installing.html pip] take in charge dependencies between
-python modules
+OBITools are deposed on the PYPI archive site, you can easily install them on your computer using the Python [pip](http://pip.readthedocs.org/en/latest/installing.html) installer. We recommend the [pip](http://pip.readthedocs.org/en/latest/installing.html) installer rather than the \`easy\_install\` one as [pip](http://pip.readthedocs.org/en/latest/installing.html) take in charge dependencies between python modules
 
-For a full description of the installation procedure, please consult the [http://metabarcoding.org/obitools/doc/wolves.html OBITools documentation].
+For a full description of the installation procedure, please consult the [OBITools documentation](http://metabarcoding.org/obitools/doc/wolves.html).
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