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  DNA Metabarcoding.

They are highly related with the following softwares:

The programs evolved with our needs. They mainly provide facilities to manipulate sequence files in  Fasta and  FastQ format. Other input formats like  genbank or  embl are supported too as well as formats related to  ecoPCR.

The OBITools programs

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.

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  here

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

A complete tutorial, demonstrating how to analyse DNA metabarcoding data using OBITools is available  here

Download and install OBITools

OBITools are deposed on the PYPI archive site, you can easily install them on your computer using the Python  pip installer. We recommend the  pip installer rather than the easy_install one as  pip take in charge dependencies between python modules

For a full description of the installation procedure, please consult the  OBITools documentation.