Dataset Information

Gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks.

ABSTRACT:

Summary

For the analysis of high-throughput genomic data produced by next-generation sequencing (NGS) technologies, researchers need to identify linkage disequilibrium (LD) structure in the genome. In this work, we developed an R package gpart which provides clustering algorithms to define LD blocks or analysis units consisting of SNPs. The visualization tool in gpart can display the LD structure and gene positions for up to 20 000 SNPs in one image. The gpart functions facilitate construction of LD blocks and SNP partitions for vast amounts of genome sequencing data within reasonable time and memory limits in personal computing environments.

Availability and implementation

The R package is available at https://bioconductor.org/packages/gpart.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Kim SA

PROVIDER: S-EPMC6821423 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Publications

gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks.

Kim Sun Ah SA Brossard Myriam M Roshandel Delnaz D Paterson Andrew D AD Bull Shelley B SB Yoo Yun Joo YJ

Bioinformatics (Oxford, England) 20191101 21

<h4>Summary</h4>For the analysis of high-throughput genomic data produced by next-generation sequencing (NGS) technologies, researchers need to identify linkage disequilibrium (LD) structure in the genome. In this work, we developed an R package gpart which provides clustering algorithms to define LD blocks or analysis units consisting of SNPs. The visualization tool in gpart can display the LD structure and gene positions for up to 20 000 SNPs in one image. The gpart functions facilitate constr ...[more]

PMID: 31070701

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