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:
- ecoPCR for DNA Metabarcoding primers in silico evaluation.
- ecoPrimers for DNA Metabarcoding primers design.
- 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 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.