The heart of GATB is GATB-Core : a high-performance and low memory footprint C++ library.
GATB-Core natively provides the following operations:
|de Bruijn graph:||
The GATB-Core library serves as a layer to develop tools and pipelines to decipher NGS data:
Since GATB-Core is a software library, the audience is mainly developers interested in creating software to perform custom-made NGS data analysis tasks. Example usages are assembly tools, de novo variant detection, reads error correction, reads compression.
From a developper point of view, the GATB-Core library provides APIs for creating/loading/traversing de Bruijn graphs, counting kmers, etc. The provided APIs are intended to be simple to use and should allow easy development of new softwares.
GATB-Core is available through an open-source C++ API. Wrappers for other languages, such as Python and Java, will be available in the future (as of March, 6th, 2017: a Python Wrapper is under experimentation).
The best way to see how to use GATB-Core as a developper is first to have a look at the tutorials. In a second step, the reference documentation should give further details.