Data from: NetView P: a network visualization tool to unravel complex population structure using genome-wide SNPs
Network-based approaches are emerging as valuable tools for the analysis of complex genetic structure in both wild and captive populations. NetView P combines data quality control with the construction of population networks based on mutual k-nearest-neighbours thresholds applied to genome-wide SNPs...
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Dryad
2015
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Online Access: | https://doi.org/10.5061/dryad.p3b3f |
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fttriple:oai:gotriple.eu:50|dedup_wf_001::725a6f63d6dc7c40c9b30504b6cc1b2e 2023-05-15T15:50:47+02:00 Data from: NetView P: a network visualization tool to unravel complex population structure using genome-wide SNPs Steinig, Eike J. Neuditschko, Markus Khatkar, Mehar S. Raadsma, Herman W. Zenger, Kyall R. 2015-07-01 https://doi.org/10.5061/dryad.p3b3f en eng Dryad http://dx.doi.org/10.5061/dryad.p3b3f https://dx.doi.org/10.5061/dryad.p3b3f lic_creative-commons 10.5061/dryad.p3b3f oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:89989 oai:easy.dans.knaw.nl:easy-dataset:89989 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 re3data_____::r3d100000044 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 Captive Populations Pinctada maxima Genomics/Proteomics Bioinfomatics/Phyloinfomatics Merluccius merluccius Canis lupus Ecological Genetics Wildlife Management Population Genetics - Empirical Life sciences medicine and health care Indonesia North America Mediterranean Atlantic geo info Dataset https://vocabularies.coar-repositories.org/resource_types/c_ddb1/ 2015 fttriple https://doi.org/10.5061/dryad.p3b3f 2023-01-22T16:53:39Z Network-based approaches are emerging as valuable tools for the analysis of complex genetic structure in both wild and captive populations. NetView P combines data quality control with the construction of population networks based on mutual k-nearest-neighbours thresholds applied to genome-wide SNPs. The program is cross-platform compatible, open-source and efficiently operates on data ranging from hundreds to hundreds of thousands of SNPs through multiprocessing in Python. We used the pipeline for the analysis of pedigree data from simulated (n = 750, SNPs = 1279) and captive Silver-lipped Pearl Oysters (n = 415, SNPs = 1107), wild populations of the European Hake from the Atlantic and Mediterranean (n = 834, SNPs = 380) and Gray Wolves from North America (n = 239, SNPs = 86,103). The population networks effectively visualize large- and fine-scale genetic structure within and between populations, including family-level structure and relationships. NetView P comprises a network-based addition to other population analysis tools and provides user-friendly access to a complex network analysis pipeline through implementation in Python. Oyster DataArchive containing data for P. maxima analysis with NetView P, including wild (n = 83, SNPs = 999), captive (n = 684, SNPs = 834) and simulated (n = 3000, SNPs = 1271) genotypes, as well as input files (PED/MAP), node attributes and networks for visualization in Cytoscape.oyster_data.zip Dataset Canis lupus Unknown Hake ENVELOPE(15.612,15.612,66.797,66.797) |
institution |
Open Polar |
collection |
Unknown |
op_collection_id |
fttriple |
language |
English |
topic |
Captive Populations Pinctada maxima Genomics/Proteomics Bioinfomatics/Phyloinfomatics Merluccius merluccius Canis lupus Ecological Genetics Wildlife Management Population Genetics - Empirical Life sciences medicine and health care Indonesia North America Mediterranean Atlantic geo info |
spellingShingle |
Captive Populations Pinctada maxima Genomics/Proteomics Bioinfomatics/Phyloinfomatics Merluccius merluccius Canis lupus Ecological Genetics Wildlife Management Population Genetics - Empirical Life sciences medicine and health care Indonesia North America Mediterranean Atlantic geo info Steinig, Eike J. Neuditschko, Markus Khatkar, Mehar S. Raadsma, Herman W. Zenger, Kyall R. Data from: NetView P: a network visualization tool to unravel complex population structure using genome-wide SNPs |
topic_facet |
Captive Populations Pinctada maxima Genomics/Proteomics Bioinfomatics/Phyloinfomatics Merluccius merluccius Canis lupus Ecological Genetics Wildlife Management Population Genetics - Empirical Life sciences medicine and health care Indonesia North America Mediterranean Atlantic geo info |
description |
Network-based approaches are emerging as valuable tools for the analysis of complex genetic structure in both wild and captive populations. NetView P combines data quality control with the construction of population networks based on mutual k-nearest-neighbours thresholds applied to genome-wide SNPs. The program is cross-platform compatible, open-source and efficiently operates on data ranging from hundreds to hundreds of thousands of SNPs through multiprocessing in Python. We used the pipeline for the analysis of pedigree data from simulated (n = 750, SNPs = 1279) and captive Silver-lipped Pearl Oysters (n = 415, SNPs = 1107), wild populations of the European Hake from the Atlantic and Mediterranean (n = 834, SNPs = 380) and Gray Wolves from North America (n = 239, SNPs = 86,103). The population networks effectively visualize large- and fine-scale genetic structure within and between populations, including family-level structure and relationships. NetView P comprises a network-based addition to other population analysis tools and provides user-friendly access to a complex network analysis pipeline through implementation in Python. Oyster DataArchive containing data for P. maxima analysis with NetView P, including wild (n = 83, SNPs = 999), captive (n = 684, SNPs = 834) and simulated (n = 3000, SNPs = 1271) genotypes, as well as input files (PED/MAP), node attributes and networks for visualization in Cytoscape.oyster_data.zip |
format |
Dataset |
author |
Steinig, Eike J. Neuditschko, Markus Khatkar, Mehar S. Raadsma, Herman W. Zenger, Kyall R. |
author_facet |
Steinig, Eike J. Neuditschko, Markus Khatkar, Mehar S. Raadsma, Herman W. Zenger, Kyall R. |
author_sort |
Steinig, Eike J. |
title |
Data from: NetView P: a network visualization tool to unravel complex population structure using genome-wide SNPs |
title_short |
Data from: NetView P: a network visualization tool to unravel complex population structure using genome-wide SNPs |
title_full |
Data from: NetView P: a network visualization tool to unravel complex population structure using genome-wide SNPs |
title_fullStr |
Data from: NetView P: a network visualization tool to unravel complex population structure using genome-wide SNPs |
title_full_unstemmed |
Data from: NetView P: a network visualization tool to unravel complex population structure using genome-wide SNPs |
title_sort |
data from: netview p: a network visualization tool to unravel complex population structure using genome-wide snps |
publisher |
Dryad |
publishDate |
2015 |
url |
https://doi.org/10.5061/dryad.p3b3f |
long_lat |
ENVELOPE(15.612,15.612,66.797,66.797) |
geographic |
Hake |
geographic_facet |
Hake |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_source |
10.5061/dryad.p3b3f oai:services.nod.dans.knaw.nl:Products/dans:oai:easy.dans.knaw.nl:easy-dataset:89989 oai:easy.dans.knaw.nl:easy-dataset:89989 10|openaire____::9e3be59865b2c1c335d32dae2fe7b254 10|re3data_____::94816e6421eeb072e7742ce6a9decc5f 10|eurocrisdris::fe4903425d9040f680d8610d9079ea14 re3data_____::r3d100000044 10|re3data_____::84e123776089ce3c7a33db98d9cd15a8 10|openaire____::081b82f96300b6a6e3d282bad31cb6e2 |
op_relation |
http://dx.doi.org/10.5061/dryad.p3b3f https://dx.doi.org/10.5061/dryad.p3b3f |
op_rights |
lic_creative-commons |
op_doi |
https://doi.org/10.5061/dryad.p3b3f |
_version_ |
1766385804341411840 |