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:

maclogo MacOS-X 10.8 or above.
(Intel 64bit processors)
Download
linuxlogo 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

cpp-github-logo 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

License

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

Change log

Have a look at this page.

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