gpart

The software tool "gpart" is for the analysis of high-throughput genomic data generated by next-generation sequencing (NGS) technologies, with a focus on identifying linkage disequilibrium (LD) structures in the genome. The R package provides clustering algorithms to define LD blocks or analysis units of single nucleotide polymorphisms (SNPs). The visualization tool in gpart can display the LD structure and gene positions for up to 20,000 SNPs in a single image.
Key functionalities of gpart include the construction of LD blocks and SNP partitions, facilitating the analysis of vast amounts of genome sequencing data. Importantly, these functions are optimized to operate within reasonable time and memory limits in personal computing environments.

Topic

DNA polymorphism;Mapping;Sequencing

Detail

  • Operation: Genotyping;Linkage disequilibrium calculation;SNP detection

  • Software interface: Library

  • Language: R

  • License: The MIT License

  • Cost: Free

  • Version name: 1.1.3

  • Credit: The National Research Foundation of Korea (NRF) , the Canadian Institutes of Health Research (CIHR), the Canadian Statistical Sciences Institute, the Canadian Institutes of Health Research Strategic Training for Advanced Genetic Epidemiology.

  • Input: -

  • Output: -

  • Contact: Sun Ah Kim sunnyeesl@gmail.com

  • Collection: -

  • Maturity: -

Publications

  • gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks.
  • Kim SA, et al. gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks. gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks. 2019; 35:4419-4421. doi: 10.1093/bioinformatics/btz308
  • https://doi.org/10.1093/BIOINFORMATICS/BTZ308
  • PMID: 31070701
  • PMC: PMC6821423

Download and documentation

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