OBITools is a set of python scripts developed to simplify the manipulation of sequence files in our labs. They were mainly designed to help us analyze Next Generation Sequencer outputs (454 or solexa) in the context of DNA Metabarcoding. These scripts rely on a Python library of the same name ''obitools''.
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 library and the scripts evolved with our needs. They mainly provide facilities to manipulate sequence files in Fasta format. Other formats are supported as genbank or embl.
The OBITools scripts 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 scripts using the pipe mecanism.
All these scripts have a -h option printing a small online help to describe the different options accepted by the script.
If an option is shared by several scripts, this option is named by the same letter in all these scripts. This is done to facilitate the usage of the OBITools scripts. In the same way, usually the name of a script begins with a prefix indicating the format of the input file.