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GDC specifications

Information


Unique identifier OMICS_00958
Name GDC
Alternative name Genome Differential Compressor
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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Publications for Genome Differential Compressor

GDC in publications

 (4)
PMCID: 4589410
PMID: 26422374
DOI: 10.1371/journal.pone.0139000

[…] against ref. in this case, the factorization can be computed using standard factorization algorithms, e.g. [–]. implementations of compression algorithms against a single reference, e.g. gdc [] and rlz [], can be applied to multiple references in a similar way. the major limitation of these algorithms/implementations is that similarities between references are left unexploited. […]

PMCID: 4493149
PMID: 26146838
DOI: 10.1371/journal.pone.0132460

[…] smaller than the original. non-referential approaches achieve ratios of up to 8:1 []., several tools implement referential compression, and some of them are noteworthy, namely: dnazip [], rlz [], gdc [] and fresco []. dnazip is one of the pioneers in this approach, and the other mentioned solutions optimized and advanced the topic at their launching time. the main differences […]

PMCID: 3868316
PMID: 24252160
DOI: 10.1186/1748-7188-8-25

[…] previous match. this handles typical differences in genomes of the same species (short insertions or deletions, snps) in an efficient manner. such an approach is successful: the related compressor, gdc [], obtains in its strongest mode the compression ratio of 1,000 for relatively encoded genomes in a collection of 70 human individuals, with decompression speed of 150 mb/s. the key ideas in gdc […]

PMCID: 3541066
PMID: 23146997
DOI: 10.1186/1748-7188-7-30

[…] which is roughly competitive to existing relative compression schemes for human genome sequences. rlz obtains a compression ration of 80:1 and rlzopt a compression ratio of 133:1 for human genomes. gdc achieves compression ratios of 200:1 - 500:1, depending on speed-tradeoffs. there exists one variant gdc-ultra, which achieves a compression ratio of 1000:1, which switches the reference sequence […]


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GDC institution(s)
Institute of Informatics, Silesian University of Technology, Gliwice, Poland; Department of Computer Engineering, Technical University of Lodz, Lodz, Poland
GDC funding source(s)
The Polish National Science Centre under the project DEC-2011/03/B/ST6/01588; The infrastructure supported by POIG.02.03.01-24-099/13 grant: ‘GeCONiI—Upper Silesian Center for Computational Science and Engineering’

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