PopHuman: the human population genomics browser

Casillas, Sònia; Mulet, Roger; Villegas Mirón, Pablo; Hervas, Sergi; Sanz, Esteve; Velasco, Daniel; Bertranpetit, Jaume, 1952-; Laayouni, Hafid, 1968-; Barbadilla, Antonio

doi:http://dx.doi.org/10.1093/nar/gkx943

PopHuman: the human population genomics browser

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Citation

Casillas S, Mulet R, Villegas-Mirón P, Hervas S, Sanz E, Velasco D, et al. PopHuman: the human population genomics browser. Nucleic Acids Res. 2018 Jan 4;46(D1):D1003-D1010. DOI: 10.1093/nar/gkx943

Abstract

The 1000 Genomes Project (1000GP) represents the most comprehensive world-wide nucleotide variation data set so far in humans, providing the sequencing and analysis of 2504 genomes from 26 populations and reporting >84 million variants. The availability of this sequence data provides the human lineage with an invaluable resource for population genomics studies, allowing the testing of molecular population genetics hypotheses and eventually the understanding of the evolutionary dynamics of genetic variation in human populations. Here we present PopHuman, a new population genomics-oriented genome browser based on JBrowse that allows the interactive visualization and retrieval of an extensive inventory of population genetics metrics. Efficient and reliable parameter estimates have been computed using a novel pipeline that faces the unique features and limitations of the 1000GP data, and include a battery of nucleotide variation measures, divergence and linkage disequilibrium parameters, as well as different tests of neutrality, estimated in non-overlapping windows along the chromosomes and in annotated genes for all 26 populations of the 1000GP. PopHuman is open and freely available at http://pophuman.uab.cat.