GDC

GDC compresses large collections of complete genomic sequences to enable efficient storage and transfer of high-throughput sequencing data.

Key Features:

• Algorithm: An algorithm specifically developed to compress extensive collections of complete genomic sequences.
• Compression ratio: Achieves compression ratios of approximately 9,500-fold on a collection of 1,092 human diploid genomes (PMID: 26108279), reported to be about fourfold better than other genomic compressors.
• Throughput: Processes data at approximately 200 megabytes per second on a modern workstation.
• Demonstrated example: Compresses ~6.7 terabytes of uncompressed FASTA from 1,092 human genomes to roughly 700 megabytes in the reported study.
• Data types and formats: Tailored to genomic sequences from high-throughput genome sequencing and demonstrated on FASTA files.
• Source code: Source code is publicly available at http://sun.aei.polsl.pl/REFRESH/index.php?page=projects&project=gdc&subpage=about.

Scientific Applications:

• Population genetics: Enables compact storage and sharing of large cohort whole-genome collections for population-scale analyses.
• Personalized medicine: Reduces storage and transfer burden for clinical and research sequencing data used in personalized medicine initiatives.
• Large-scale bioinformatics projects: Facilitates efficient data management and network transfer of many complete genomes in genomics research projects.

Methodology:

Implements advanced compression techniques tailored to genomic sequences as described in the referenced study (PMID: 26108279).