GATB: Genome Assembly & Analysis Tool Box.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 24990603.
- Also identified by DOI 10.1093/bioinformatics/btu406 and PMC identifier 4184257.
- Licence recorded as CC BY-NC.
- Because redistribution is not established, this page shows the abstract only. Follow the links below for the full text.
Abstract
Efficient and fast next-generation sequencing (NGS) algorithms are essential to analyze the terabytes of data generated by the NGS machines. A serious bottleneck can be the design of such algorithms, as they require sophisticated data structures and advanced hardware implementation. We propose an open-source library dedicated to genome assembly and analysis to fasten the process of developing efficient software. The library is based on a recent optimized de-Bruijn graph implementation allowing complex genomes to be processed on desktop computers using fast algorithms with low memory footprints. The GATB library is written in C++ and is available at the following Web site http://gatb.inria.fr under the A-GPL license. lavenier@irisa.fr Supplementary data are available at Bioinformatics online.
Medical subject headings
- Biostatistics
- Genomics
- High-Throughput Nucleotide Sequencing
- Software