DivStat: a user-friendly tool for single nucleotide polymorphism analysis of genomic diversity

Inês Soares; Ana Moleirinho; Gonçalo N P Oliveira; António Amorim

doi:10.1371/journal.pone.0119851

DivStat: a user-friendly tool for single nucleotide polymorphism analysis of genomic diversity

PLoS One. 2015 Mar 10;10(3):e0119851. doi: 10.1371/journal.pone.0119851. eCollection 2015.

Authors

Inês Soares¹, Ana Moleirinho², Gonçalo N P Oliveira³, António Amorim²

Affiliations

¹ IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal.
² IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Rua Dr. Roberto Frias s/n, 4200-465, Porto, Portugal; Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.
³ Faculty of Sciences, University of Porto, Rua do Campo Alegre s/n, 4169-007, Porto, Portugal; IFIMUP and IN-Institute of Nanoscience and Nanotechnology, Rua do Campo Alegre, 687, 4169-007, Porto, Portugal.

Abstract

Recent developments have led to an enormous increase of publicly available large genomic data, including complete genomes. The 1000 Genomes Project was a major contributor, releasing the results of sequencing a large number of individual genomes, and allowing for a myriad of large scale studies on human genetic variation. However, the tools currently available are insufficient when the goal concerns some analyses of data sets encompassing more than hundreds of base pairs and when considering haplotype sequences of single nucleotide polymorphisms (SNPs). Here, we present a new and potent tool to deal with large data sets allowing the computation of a variety of summary statistics of population genetic data, increasing the speed of data analysis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Databases, Genetic
Genome, Human
Haplotypes
Humans
Polymorphism, Single Nucleotide
Sequence Analysis, DNA
Software*

Grants and funding

This work was supported by the Portuguese Foundation for Science and Technology (FCT) fellowship (SFRH/BD/73508/2010) to A. M. IPATIMUP is an Associate Laboratory of the Portuguese Ministry of Science, Technology and Higher Education and is partly supported by FCT. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.