Improving ancient DNA read mapping against modern reference genomes View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2012-12

AUTHORS

Mikkel Schubert, Aurelien Ginolhac, Stinus Lindgreen, John F Thompson, Khaled AS AL-Rasheid, Eske Willerslev, Anders Krogh, Ludovic Orlando

ABSTRACT

BACKGROUND: Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic material from long-dead organisms is still complicated by a number of issues, including post-mortem DNA damage and high levels of environmental contamination. Together with error profiles specific to the type of sequencing platforms used, these specificities could limit our ability to map sequencing reads against modern reference genomes and therefore limit our ability to identify endogenous ancient reads, reducing the efficiency of shotgun sequencing aDNA. RESULTS: In this study, we compare different computational methods for improving the accuracy and sensitivity of aDNA sequence identification, based on shotgun sequencing reads recovered from Pleistocene horse extracts using Illumina GAIIx and Helicos Heliscope platforms. We show that the performance of the Burrows Wheeler Aligner (BWA), that has been developed for mapping of undamaged sequencing reads using platforms with low rates of indel-types of sequencing errors, can be employed at acceptable run-times by modifying default parameters in a platform-specific manner. We also examine if trimming likely damaged positions at read ends can increase the recovery of genuine aDNA fragments and if accurate identification of human contamination can be achieved using a strategy previously suggested based on best hit filtering. We show that combining our different mapping and filtering approaches can increase the number of high-quality endogenous hits recovered by up to 33%. CONCLUSIONS: We have shown that Illumina and Helicos sequences recovered from aDNA extracts could not be aligned to modern reference genomes with the same efficiency unless mapping parameters are optimized for the specific types of errors generated by these platforms and by post-mortem DNA damage. Our findings have important implications for future aDNA research, as we define mapping guidelines that improve our ability to identify genuine aDNA sequences, which in turn could improve the genotyping accuracy of ancient specimens. Our framework provides a significant improvement to the standard procedures used for characterizing ancient genomes, which is challenged by contamination and often low amounts of DNA material. More... »

PAGES

178

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/1471-2164-13-178

DOI

http://dx.doi.org/10.1186/1471-2164-13-178

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1013249306

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/22574660


Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
Incoming Citations Browse incoming citations for this publication using opencitations.net

JSON-LD is the canonical representation for SciGraph data.

TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

[
  {
    "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
    "about": [
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Genetics", 
        "type": "DefinedTerm"
      }, 
      {
        "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Biological Sciences", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "DNA Damage", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Fossils", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genotype", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "High-Throughput Nucleotide Sequencing", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Humans", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Sequence Analysis, DNA", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "University of Copenhagen", 
          "id": "https://www.grid.ac/institutes/grid.5254.6", 
          "name": [
            "Centre for GeoGenetics; Natural History Museum of Denmark, University of Copenhagen, 5-7 \u00d8ster Voldgade, 1350, Kobenhavns K, Denmark", 
            "The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen, Denmark"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Schubert", 
        "givenName": "Mikkel", 
        "id": "sg:person.0774220504.34", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0774220504.34"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Copenhagen", 
          "id": "https://www.grid.ac/institutes/grid.5254.6", 
          "name": [
            "Centre for GeoGenetics; Natural History Museum of Denmark, University of Copenhagen, 5-7 \u00d8ster Voldgade, 1350, Kobenhavns K, Denmark"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ginolhac", 
        "givenName": "Aurelien", 
        "id": "sg:person.01050333103.98", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01050333103.98"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Copenhagen", 
          "id": "https://www.grid.ac/institutes/grid.5254.6", 
          "name": [
            "Centre for GeoGenetics; Natural History Museum of Denmark, University of Copenhagen, 5-7 \u00d8ster Voldgade, 1350, Kobenhavns K, Denmark", 
            "The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen, Denmark"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Lindgreen", 
        "givenName": "Stinus", 
        "id": "sg:person.0635177211.38", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0635177211.38"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Helicos Biosciences (United States)", 
          "id": "https://www.grid.ac/institutes/grid.418487.6", 
          "name": [
            "Applications, Methods and Collaborations; Helicos BioSciences, One Kendall Square Bldg 200LL, 02139, Cambridge, MA, USA", 
            "NABsys Inc, 60 Clifford Street, 02903, Providence, RI, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Thompson", 
        "givenName": "John F", 
        "id": "sg:person.014051114644.24", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014051114644.24"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "King Saud University", 
          "id": "https://www.grid.ac/institutes/grid.56302.32", 
          "name": [
            "Zoology Department, College of Science King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia"
          ], 
          "type": "Organization"
        }, 
        "familyName": "AL-Rasheid", 
        "givenName": "Khaled AS", 
        "id": "sg:person.01352355663.28", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01352355663.28"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Copenhagen", 
          "id": "https://www.grid.ac/institutes/grid.5254.6", 
          "name": [
            "Centre for GeoGenetics; Natural History Museum of Denmark, University of Copenhagen, 5-7 \u00d8ster Voldgade, 1350, Kobenhavns K, Denmark"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Willerslev", 
        "givenName": "Eske", 
        "id": "sg:person.0714231071.76", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0714231071.76"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Copenhagen", 
          "id": "https://www.grid.ac/institutes/grid.5254.6", 
          "name": [
            "Centre for GeoGenetics; Natural History Museum of Denmark, University of Copenhagen, 5-7 \u00d8ster Voldgade, 1350, Kobenhavns K, Denmark", 
            "The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen, Denmark"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Krogh", 
        "givenName": "Anders", 
        "id": "sg:person.01057515665.52", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01057515665.52"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "University of Copenhagen", 
          "id": "https://www.grid.ac/institutes/grid.5254.6", 
          "name": [
            "Centre for GeoGenetics; Natural History Museum of Denmark, University of Copenhagen, 5-7 \u00d8ster Voldgade, 1350, Kobenhavns K, Denmark"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Orlando", 
        "givenName": "Ludovic", 
        "id": "sg:person.01201152047.48", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01201152047.48"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "sg:pub.10.1186/gb-2010-11-5-r47", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000160930", 
          "https://doi.org/10.1186/gb-2010-11-5-r47"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0308391100", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1000804764"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/msq083", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001874812"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/molbev/msq083", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1001874812"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1188021", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002597304"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1188021", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1002597304"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature07446", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003406391", 
          "https://doi.org/10.1038/nature07446"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0605327103", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003805091"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.tree.2005.07.005", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003908661"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.tree.2005.07.005", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1003908661"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/0471142727.mb0710s92", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007096038"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1002/0471142727.mb0710s92", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1007096038"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bib/bbp019", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009995255"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bib/bbp019", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1009995255"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1038/emboj.2009.222", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010219128"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.122747.111", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020096058"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/j.cub.2003.12.012", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1020335334"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature08835", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021776500", 
          "https://doi.org/10.1038/nature08835"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature08835", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021776500", 
          "https://doi.org/10.1038/nature08835"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature05336", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022286131", 
          "https://doi.org/10.1038/nature05336"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature05336", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022286131", 
          "https://doi.org/10.1038/nature05336"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature05336", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1022286131", 
          "https://doi.org/10.1038/nature05336"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature08976", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025023915", 
          "https://doi.org/10.1038/nature08976"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature08976", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025023915", 
          "https://doi.org/10.1038/nature08976"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1016/s0076-6879(10)72002-4", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1027045392"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.1354", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1028638279", 
          "https://doi.org/10.1038/nmeth.1354"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkl483", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1029169829"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btr347", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030568980"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1371/journal.pone.0014004", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1031804493"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1186/1471-2164-13-177", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1032076652", 
          "https://doi.org/10.1186/1471-2164-13-177"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature10574", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1034957697", 
          "https://doi.org/10.1038/nature10574"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkp1163", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1036956881"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btp324", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038266369"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature10549", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1042284160", 
          "https://doi.org/10.1038/nature10549"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.0704665104", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1045401726"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.1105107108", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1049707959"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature09710", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050205294", 
          "https://doi.org/10.1038/nature09710"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature09710", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1050205294", 
          "https://doi.org/10.1038/nature09710"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1211177", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052025136"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/nar/gkm588", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1053124372"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1141758", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062455979"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1159750", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062457874"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1174462", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062460190"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1178158", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062460476"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2012-12", 
    "datePublishedReg": "2012-12-01", 
    "description": "BACKGROUND: Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic material from long-dead organisms is still complicated by a number of issues, including post-mortem DNA damage and high levels of environmental contamination. Together with error profiles specific to the type of sequencing platforms used, these specificities could limit our ability to map sequencing reads against modern reference genomes and therefore limit our ability to identify endogenous ancient reads, reducing the efficiency of shotgun sequencing aDNA.\nRESULTS: In this study, we compare different computational methods for improving the accuracy and sensitivity of aDNA sequence identification, based on shotgun sequencing reads recovered from Pleistocene horse extracts using Illumina GAIIx and Helicos Heliscope platforms. We show that the performance of the Burrows Wheeler Aligner (BWA), that has been developed for mapping of undamaged sequencing reads using platforms with low rates of indel-types of sequencing errors, can be employed at acceptable run-times by modifying default parameters in a platform-specific manner. We also examine if trimming likely damaged positions at read ends can increase the recovery of genuine aDNA fragments and if accurate identification of human contamination can be achieved using a strategy previously suggested based on best hit filtering. We show that combining our different mapping and filtering approaches can increase the number of high-quality endogenous hits recovered by up to 33%.\nCONCLUSIONS: We have shown that Illumina and Helicos sequences recovered from aDNA extracts could not be aligned to modern reference genomes with the same efficiency unless mapping parameters are optimized for the specific types of errors generated by these platforms and by post-mortem DNA damage. Our findings have important implications for future aDNA research, as we define mapping guidelines that improve our ability to identify genuine aDNA sequences, which in turn could improve the genotyping accuracy of ancient specimens. Our framework provides a significant improvement to the standard procedures used for characterizing ancient genomes, which is challenged by contamination and often low amounts of DNA material.", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/1471-2164-13-178", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isFundedItemOf": [
      {
        "id": "sg:grant.3784511", 
        "type": "MonetaryGrant"
      }, 
      {
        "id": "sg:grant.2669364", 
        "type": "MonetaryGrant"
      }
    ], 
    "isPartOf": [
      {
        "id": "sg:journal.1023790", 
        "issn": [
          "1471-2164"
        ], 
        "name": "BMC Genomics", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "1", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "13"
      }
    ], 
    "name": "Improving ancient DNA read mapping against modern reference genomes", 
    "pagination": "178", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "3f1e7782d773028a54ef98a8f4bb465cebff195a65e251830e0a7b8f43e4c23c"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "22574660"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "100965258"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/1471-2164-13-178"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1013249306"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/1471-2164-13-178", 
      "https://app.dimensions.ai/details/publication/pub.1013249306"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-10T14:07", 
    "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
    "sdPublisher": {
      "name": "Springer Nature - SN SciGraph project", 
      "type": "Organization"
    }, 
    "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8660_00000504.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1186%2F1471-2164-13-178"
  }
]
 

Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

JSON-LD is a popular format for linked data which is fully compatible with JSON.

curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-13-178'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-13-178'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-13-178'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/1471-2164-13-178'


 

This table displays all metadata directly associated to this object as RDF triples.

265 TRIPLES      21 PREDICATES      69 URIs      27 LITERALS      15 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/1471-2164-13-178 schema:about N704de93331b14109bd705841f7188e94
2 N75530daf9aaf49e2bfd4add721203b89
3 N8d604da4b3424e0dbcd9272ad1be5225
4 N9fdd0125995a418cb302da654ae3655b
5 Nd5507bdeeaca4ef6a29b8b677f0ca5c2
6 Nefd00cd4e1d844d98761a4432579aa54
7 anzsrc-for:06
8 anzsrc-for:0604
9 schema:author Nc3269e80a01f4786a0f7eb90f6436b4b
10 schema:citation sg:pub.10.1038/nature05336
11 sg:pub.10.1038/nature07446
12 sg:pub.10.1038/nature08835
13 sg:pub.10.1038/nature08976
14 sg:pub.10.1038/nature09710
15 sg:pub.10.1038/nature10549
16 sg:pub.10.1038/nature10574
17 sg:pub.10.1038/nmeth.1354
18 sg:pub.10.1186/1471-2164-13-177
19 sg:pub.10.1186/gb-2010-11-5-r47
20 https://doi.org/10.1002/0471142727.mb0710s92
21 https://doi.org/10.1016/j.cub.2003.12.012
22 https://doi.org/10.1016/j.tree.2005.07.005
23 https://doi.org/10.1016/s0076-6879(10)72002-4
24 https://doi.org/10.1038/emboj.2009.222
25 https://doi.org/10.1073/pnas.0308391100
26 https://doi.org/10.1073/pnas.0605327103
27 https://doi.org/10.1073/pnas.0704665104
28 https://doi.org/10.1073/pnas.1105107108
29 https://doi.org/10.1093/bib/bbp019
30 https://doi.org/10.1093/bioinformatics/btp324
31 https://doi.org/10.1093/bioinformatics/btr347
32 https://doi.org/10.1093/molbev/msq083
33 https://doi.org/10.1093/nar/gkl483
34 https://doi.org/10.1093/nar/gkm588
35 https://doi.org/10.1093/nar/gkp1163
36 https://doi.org/10.1101/gr.122747.111
37 https://doi.org/10.1126/science.1141758
38 https://doi.org/10.1126/science.1159750
39 https://doi.org/10.1126/science.1174462
40 https://doi.org/10.1126/science.1178158
41 https://doi.org/10.1126/science.1188021
42 https://doi.org/10.1126/science.1211177
43 https://doi.org/10.1371/journal.pone.0014004
44 schema:datePublished 2012-12
45 schema:datePublishedReg 2012-12-01
46 schema:description BACKGROUND: Next-Generation Sequencing has revolutionized our approach to ancient DNA (aDNA) research, by providing complete genomic sequences of ancient individuals and extinct species. However, the recovery of genetic material from long-dead organisms is still complicated by a number of issues, including post-mortem DNA damage and high levels of environmental contamination. Together with error profiles specific to the type of sequencing platforms used, these specificities could limit our ability to map sequencing reads against modern reference genomes and therefore limit our ability to identify endogenous ancient reads, reducing the efficiency of shotgun sequencing aDNA. RESULTS: In this study, we compare different computational methods for improving the accuracy and sensitivity of aDNA sequence identification, based on shotgun sequencing reads recovered from Pleistocene horse extracts using Illumina GAIIx and Helicos Heliscope platforms. We show that the performance of the Burrows Wheeler Aligner (BWA), that has been developed for mapping of undamaged sequencing reads using platforms with low rates of indel-types of sequencing errors, can be employed at acceptable run-times by modifying default parameters in a platform-specific manner. We also examine if trimming likely damaged positions at read ends can increase the recovery of genuine aDNA fragments and if accurate identification of human contamination can be achieved using a strategy previously suggested based on best hit filtering. We show that combining our different mapping and filtering approaches can increase the number of high-quality endogenous hits recovered by up to 33%. CONCLUSIONS: We have shown that Illumina and Helicos sequences recovered from aDNA extracts could not be aligned to modern reference genomes with the same efficiency unless mapping parameters are optimized for the specific types of errors generated by these platforms and by post-mortem DNA damage. Our findings have important implications for future aDNA research, as we define mapping guidelines that improve our ability to identify genuine aDNA sequences, which in turn could improve the genotyping accuracy of ancient specimens. Our framework provides a significant improvement to the standard procedures used for characterizing ancient genomes, which is challenged by contamination and often low amounts of DNA material.
47 schema:genre research_article
48 schema:inLanguage en
49 schema:isAccessibleForFree true
50 schema:isPartOf N171596482a5347d0a98fe3fe5d12ee12
51 Nbe340981fa034182ac739efcdc156d77
52 sg:journal.1023790
53 schema:name Improving ancient DNA read mapping against modern reference genomes
54 schema:pagination 178
55 schema:productId N46192c3be94740aaa1e106b110e3429d
56 Nbe42443adee943058522d8b008895627
57 Nd22abd572dac442b80480d8527b2ae8e
58 Ndfa6e65f1ab04042958780fa001bb287
59 Ne7620e0ed1b942f0a158a3067cc518ca
60 schema:sameAs https://app.dimensions.ai/details/publication/pub.1013249306
61 https://doi.org/10.1186/1471-2164-13-178
62 schema:sdDatePublished 2019-04-10T14:07
63 schema:sdLicense https://scigraph.springernature.com/explorer/license/
64 schema:sdPublisher N8b2c02b81ecb41ba898a9c96f4615141
65 schema:url http://link.springer.com/10.1186%2F1471-2164-13-178
66 sgo:license sg:explorer/license/
67 sgo:sdDataset articles
68 rdf:type schema:ScholarlyArticle
69 N171596482a5347d0a98fe3fe5d12ee12 schema:volumeNumber 13
70 rdf:type schema:PublicationVolume
71 N46192c3be94740aaa1e106b110e3429d schema:name pubmed_id
72 schema:value 22574660
73 rdf:type schema:PropertyValue
74 N4f3b93bd5bf54b5db191c9fedd2cf122 rdf:first sg:person.01057515665.52
75 rdf:rest Nd3088bb4c50743e2aa48cbd2fc2629a2
76 N6917ac24614a49f7b5dfb43dbe567f9a rdf:first sg:person.014051114644.24
77 rdf:rest N8625101d69304289a15722b096400a3a
78 N6f36688798e342eb9c3e9656d4a641cb rdf:first sg:person.0714231071.76
79 rdf:rest N4f3b93bd5bf54b5db191c9fedd2cf122
80 N704de93331b14109bd705841f7188e94 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
81 schema:name Genotype
82 rdf:type schema:DefinedTerm
83 N75530daf9aaf49e2bfd4add721203b89 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
84 schema:name Humans
85 rdf:type schema:DefinedTerm
86 N8138f17239c44ca19597d259a07593c4 rdf:first sg:person.0635177211.38
87 rdf:rest N6917ac24614a49f7b5dfb43dbe567f9a
88 N8625101d69304289a15722b096400a3a rdf:first sg:person.01352355663.28
89 rdf:rest N6f36688798e342eb9c3e9656d4a641cb
90 N8b2c02b81ecb41ba898a9c96f4615141 schema:name Springer Nature - SN SciGraph project
91 rdf:type schema:Organization
92 N8d604da4b3424e0dbcd9272ad1be5225 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
93 schema:name Fossils
94 rdf:type schema:DefinedTerm
95 N96f43cdefa9d45fbbb173792d3103ea7 rdf:first sg:person.01050333103.98
96 rdf:rest N8138f17239c44ca19597d259a07593c4
97 N9fdd0125995a418cb302da654ae3655b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
98 schema:name DNA Damage
99 rdf:type schema:DefinedTerm
100 Nbe340981fa034182ac739efcdc156d77 schema:issueNumber 1
101 rdf:type schema:PublicationIssue
102 Nbe42443adee943058522d8b008895627 schema:name nlm_unique_id
103 schema:value 100965258
104 rdf:type schema:PropertyValue
105 Nc3269e80a01f4786a0f7eb90f6436b4b rdf:first sg:person.0774220504.34
106 rdf:rest N96f43cdefa9d45fbbb173792d3103ea7
107 Nd22abd572dac442b80480d8527b2ae8e schema:name doi
108 schema:value 10.1186/1471-2164-13-178
109 rdf:type schema:PropertyValue
110 Nd3088bb4c50743e2aa48cbd2fc2629a2 rdf:first sg:person.01201152047.48
111 rdf:rest rdf:nil
112 Nd5507bdeeaca4ef6a29b8b677f0ca5c2 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
113 schema:name High-Throughput Nucleotide Sequencing
114 rdf:type schema:DefinedTerm
115 Ndfa6e65f1ab04042958780fa001bb287 schema:name dimensions_id
116 schema:value pub.1013249306
117 rdf:type schema:PropertyValue
118 Ne7620e0ed1b942f0a158a3067cc518ca schema:name readcube_id
119 schema:value 3f1e7782d773028a54ef98a8f4bb465cebff195a65e251830e0a7b8f43e4c23c
120 rdf:type schema:PropertyValue
121 Nefd00cd4e1d844d98761a4432579aa54 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
122 schema:name Sequence Analysis, DNA
123 rdf:type schema:DefinedTerm
124 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
125 schema:name Biological Sciences
126 rdf:type schema:DefinedTerm
127 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
128 schema:name Genetics
129 rdf:type schema:DefinedTerm
130 sg:grant.2669364 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2164-13-178
131 rdf:type schema:MonetaryGrant
132 sg:grant.3784511 http://pending.schema.org/fundedItem sg:pub.10.1186/1471-2164-13-178
133 rdf:type schema:MonetaryGrant
134 sg:journal.1023790 schema:issn 1471-2164
135 schema:name BMC Genomics
136 rdf:type schema:Periodical
137 sg:person.01050333103.98 schema:affiliation https://www.grid.ac/institutes/grid.5254.6
138 schema:familyName Ginolhac
139 schema:givenName Aurelien
140 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01050333103.98
141 rdf:type schema:Person
142 sg:person.01057515665.52 schema:affiliation https://www.grid.ac/institutes/grid.5254.6
143 schema:familyName Krogh
144 schema:givenName Anders
145 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01057515665.52
146 rdf:type schema:Person
147 sg:person.01201152047.48 schema:affiliation https://www.grid.ac/institutes/grid.5254.6
148 schema:familyName Orlando
149 schema:givenName Ludovic
150 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01201152047.48
151 rdf:type schema:Person
152 sg:person.01352355663.28 schema:affiliation https://www.grid.ac/institutes/grid.56302.32
153 schema:familyName AL-Rasheid
154 schema:givenName Khaled AS
155 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01352355663.28
156 rdf:type schema:Person
157 sg:person.014051114644.24 schema:affiliation https://www.grid.ac/institutes/grid.418487.6
158 schema:familyName Thompson
159 schema:givenName John F
160 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.014051114644.24
161 rdf:type schema:Person
162 sg:person.0635177211.38 schema:affiliation https://www.grid.ac/institutes/grid.5254.6
163 schema:familyName Lindgreen
164 schema:givenName Stinus
165 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0635177211.38
166 rdf:type schema:Person
167 sg:person.0714231071.76 schema:affiliation https://www.grid.ac/institutes/grid.5254.6
168 schema:familyName Willerslev
169 schema:givenName Eske
170 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0714231071.76
171 rdf:type schema:Person
172 sg:person.0774220504.34 schema:affiliation https://www.grid.ac/institutes/grid.5254.6
173 schema:familyName Schubert
174 schema:givenName Mikkel
175 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0774220504.34
176 rdf:type schema:Person
177 sg:pub.10.1038/nature05336 schema:sameAs https://app.dimensions.ai/details/publication/pub.1022286131
178 https://doi.org/10.1038/nature05336
179 rdf:type schema:CreativeWork
180 sg:pub.10.1038/nature07446 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003406391
181 https://doi.org/10.1038/nature07446
182 rdf:type schema:CreativeWork
183 sg:pub.10.1038/nature08835 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021776500
184 https://doi.org/10.1038/nature08835
185 rdf:type schema:CreativeWork
186 sg:pub.10.1038/nature08976 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025023915
187 https://doi.org/10.1038/nature08976
188 rdf:type schema:CreativeWork
189 sg:pub.10.1038/nature09710 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050205294
190 https://doi.org/10.1038/nature09710
191 rdf:type schema:CreativeWork
192 sg:pub.10.1038/nature10549 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042284160
193 https://doi.org/10.1038/nature10549
194 rdf:type schema:CreativeWork
195 sg:pub.10.1038/nature10574 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034957697
196 https://doi.org/10.1038/nature10574
197 rdf:type schema:CreativeWork
198 sg:pub.10.1038/nmeth.1354 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028638279
199 https://doi.org/10.1038/nmeth.1354
200 rdf:type schema:CreativeWork
201 sg:pub.10.1186/1471-2164-13-177 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032076652
202 https://doi.org/10.1186/1471-2164-13-177
203 rdf:type schema:CreativeWork
204 sg:pub.10.1186/gb-2010-11-5-r47 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000160930
205 https://doi.org/10.1186/gb-2010-11-5-r47
206 rdf:type schema:CreativeWork
207 https://doi.org/10.1002/0471142727.mb0710s92 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007096038
208 rdf:type schema:CreativeWork
209 https://doi.org/10.1016/j.cub.2003.12.012 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020335334
210 rdf:type schema:CreativeWork
211 https://doi.org/10.1016/j.tree.2005.07.005 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003908661
212 rdf:type schema:CreativeWork
213 https://doi.org/10.1016/s0076-6879(10)72002-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027045392
214 rdf:type schema:CreativeWork
215 https://doi.org/10.1038/emboj.2009.222 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010219128
216 rdf:type schema:CreativeWork
217 https://doi.org/10.1073/pnas.0308391100 schema:sameAs https://app.dimensions.ai/details/publication/pub.1000804764
218 rdf:type schema:CreativeWork
219 https://doi.org/10.1073/pnas.0605327103 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003805091
220 rdf:type schema:CreativeWork
221 https://doi.org/10.1073/pnas.0704665104 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045401726
222 rdf:type schema:CreativeWork
223 https://doi.org/10.1073/pnas.1105107108 schema:sameAs https://app.dimensions.ai/details/publication/pub.1049707959
224 rdf:type schema:CreativeWork
225 https://doi.org/10.1093/bib/bbp019 schema:sameAs https://app.dimensions.ai/details/publication/pub.1009995255
226 rdf:type schema:CreativeWork
227 https://doi.org/10.1093/bioinformatics/btp324 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038266369
228 rdf:type schema:CreativeWork
229 https://doi.org/10.1093/bioinformatics/btr347 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030568980
230 rdf:type schema:CreativeWork
231 https://doi.org/10.1093/molbev/msq083 schema:sameAs https://app.dimensions.ai/details/publication/pub.1001874812
232 rdf:type schema:CreativeWork
233 https://doi.org/10.1093/nar/gkl483 schema:sameAs https://app.dimensions.ai/details/publication/pub.1029169829
234 rdf:type schema:CreativeWork
235 https://doi.org/10.1093/nar/gkm588 schema:sameAs https://app.dimensions.ai/details/publication/pub.1053124372
236 rdf:type schema:CreativeWork
237 https://doi.org/10.1093/nar/gkp1163 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036956881
238 rdf:type schema:CreativeWork
239 https://doi.org/10.1101/gr.122747.111 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020096058
240 rdf:type schema:CreativeWork
241 https://doi.org/10.1126/science.1141758 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062455979
242 rdf:type schema:CreativeWork
243 https://doi.org/10.1126/science.1159750 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062457874
244 rdf:type schema:CreativeWork
245 https://doi.org/10.1126/science.1174462 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062460190
246 rdf:type schema:CreativeWork
247 https://doi.org/10.1126/science.1178158 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062460476
248 rdf:type schema:CreativeWork
249 https://doi.org/10.1126/science.1188021 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002597304
250 rdf:type schema:CreativeWork
251 https://doi.org/10.1126/science.1211177 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052025136
252 rdf:type schema:CreativeWork
253 https://doi.org/10.1371/journal.pone.0014004 schema:sameAs https://app.dimensions.ai/details/publication/pub.1031804493
254 rdf:type schema:CreativeWork
255 https://www.grid.ac/institutes/grid.418487.6 schema:alternateName Helicos Biosciences (United States)
256 schema:name Applications, Methods and Collaborations; Helicos BioSciences, One Kendall Square Bldg 200LL, 02139, Cambridge, MA, USA
257 NABsys Inc, 60 Clifford Street, 02903, Providence, RI, USA
258 rdf:type schema:Organization
259 https://www.grid.ac/institutes/grid.5254.6 schema:alternateName University of Copenhagen
260 schema:name Centre for GeoGenetics; Natural History Museum of Denmark, University of Copenhagen, 5-7 Øster Voldgade, 1350, Kobenhavns K, Denmark
261 The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen, Denmark
262 rdf:type schema:Organization
263 https://www.grid.ac/institutes/grid.56302.32 schema:alternateName King Saud University
264 schema:name Zoology Department, College of Science King Saud University, P.O. Box 2455, 11451, Riyadh, Saudi Arabia
265 rdf:type schema:Organization
 




Preview window. Press ESC to close (or click here)


...