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Patrick Durand edited this page May 19, 2017
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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.
Start your discovery of the library with:
In addition, feel free to contact the GATB-Core devel team if you have any questions regarding the use of the library.