TY - JOUR
T1 - PopHuman
T2 - The human population genomics browser
AU - Casillas, Sònia
AU - Mulet, Roger
AU - Villegas-Mirón, Pablo
AU - Hervas, Sergi
AU - Sanz, Esteve
AU - Velasco, Daniel
AU - Bertranpetit, Jaume
AU - Laayouni, Hafid
AU - Barbadilla, Antonio
N1 - Publisher Copyright:
© 2017 The Author(s).
PY - 2018/1/1
Y1 - 2018/1/1
N2 - The 1000 Genomes Project (1000GP) represents the most comprehensiveworld-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 geneticsmetrics. 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.
AB - The 1000 Genomes Project (1000GP) represents the most comprehensiveworld-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 geneticsmetrics. 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.
UR - http://www.scopus.com/inward/record.url?scp=85040936901&partnerID=8YFLogxK
U2 - 10.1093/nar/gkx943
DO - 10.1093/nar/gkx943
M3 - Article
C2 - 29059408
SN - 0305-1048
VL - 46
SP - D1003-D1010
JO - Nucleic Acids Research
JF - Nucleic Acids Research
IS - D1
ER -