GATB-CORE

You can use the GATB-Core library to develop new NGS data analysis softwares.

GATB-Core natively provides the following high-performance and memory-efficient operations:

Reads handling:	FASTA/FASTQ parsing; FASTA writing Parallel iteration of sequences
K-mer:	K-mer counting Minimizer computation of k-mers, partitioning of datasets by minimizers Bloom data structure of k-mers Hash table of k-mers Minimal perfect hash function of k-mers Arbitrarily large k-mers representations
de Bruijn graph:	graph construction graph traversal operations (contigs, unitigs) graph simplifications for assembly (tip removal, bulge removal)

The GATB-CORE library is intended to be used by developers having skills in c programming (see documentation, below).

Binaries

GATB-CORE is available as a binary library for immediate compiling and linking on Linux and MacOSX platforms, with the following requirements:

	MacOS-X 10.8 or above. (Intel 64bit processors)	Download
	Linux running on Intel or AMD 64bit processors. (kernel 2.6.32 or above, GLIBCXX_3.4.13 or above)	Download

For all other platforms or configurations, or if above binaries fail to run on your computer, you should download source code and compile it.

Source Code

GATB-CORE library is fully written in C .

Download

Documentation

Key Concepts

• GATB in a nutshell: very short introduction to the GATB project
• Overview: general overview of the GATB project with some key concepts

Learn and Make Software Tools with GATB-CORE

• GATB Tutorial: an online interactive tutorial to learn GATB-Core API
• API documentation: the complete documentation on GATB-CORE c API
• Setup Eclipse c IDE (Linux) to work with GATB-Core library
• Setup Xcode IDE (MasOSX) to work with GATB-Core library

License

GATB binaries and source code are covered by the Affero GPL version 3 license.

Change log

Have a look at this page.