ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2009-10

AUTHORS

Iain MacCallum, Dariusz Przybylski, Sante Gnerre, Joshua Burton, Ilya Shlyakhter, Andreas Gnirke, Joel Malek, Kevin McKernan, Swati Ranade, Terrance P Shea, Louise Williams, Sarah Young, Chad Nusbaum, David B Jaffe

ABSTRACT

We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes of varied GC composition and sizes up to 40 Mb, ALLPATHS2 generated assemblies with long, accurate contigs and scaffolds. Velvet and EULER-SR were less accurate. For example, for Escherichia coli, the fraction of 10-kb stretches that were perfect was 99.8% (ALLPATHS2), 68.7% (Velvet), and 42.1% (EULER-SR). More... »

PAGES

r103

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/gb-2009-10-10-r103

DOI

http://dx.doi.org/10.1186/gb-2009-10-10-r103

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1012804464

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/19796385


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/2008/0605", 
        "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
        "name": "Microbiology", 
        "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": "Bacteria", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Base Pairing", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Fungi", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genome", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Genomics", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Reproducibility of Results", 
        "type": "DefinedTerm"
      }, 
      {
        "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
        "name": "Software", 
        "type": "DefinedTerm"
      }
    ], 
    "author": [
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Charles Street, 02141, Cambridge, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "MacCallum", 
        "givenName": "Iain", 
        "id": "sg:person.01057437731.69", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01057437731.69"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Charles Street, 02141, Cambridge, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Przybylski", 
        "givenName": "Dariusz", 
        "id": "sg:person.01127255432.56", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01127255432.56"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Charles Street, 02141, Cambridge, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Gnerre", 
        "givenName": "Sante", 
        "id": "sg:person.0761567341.00", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0761567341.00"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Charles Street, 02141, Cambridge, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Burton", 
        "givenName": "Joshua", 
        "id": "sg:person.01171316726.17", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01171316726.17"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Charles Street, 02141, Cambridge, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Shlyakhter", 
        "givenName": "Ilya", 
        "id": "sg:person.0625052656.12", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0625052656.12"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Charles Street, 02141, Cambridge, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Gnirke", 
        "givenName": "Andreas", 
        "id": "sg:person.0645200471.91", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0645200471.91"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Weill Cornell Medical College in Qatar", 
          "id": "https://www.grid.ac/institutes/grid.416973.e", 
          "name": [
            "Life Technologies, Cummings Center, 01915, Beverly, MA, USA", 
            "Department of Medical Genetics, Weill Cornell Medical College in Qatar, Al-Rayaan St., 24144, Doha, Qatar"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Malek", 
        "givenName": "Joel", 
        "id": "sg:person.01252210540.25", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01252210540.25"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Thermo Fisher Scientific (United States)", 
          "id": "https://www.grid.ac/institutes/grid.418190.5", 
          "name": [
            "Life Technologies, Cummings Center, 01915, Beverly, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "McKernan", 
        "givenName": "Kevin", 
        "id": "sg:person.0614733731.46", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0614733731.46"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Pacific Biosciences (United States)", 
          "id": "https://www.grid.ac/institutes/grid.423340.2", 
          "name": [
            "Life Technologies, Cummings Center, 01915, Beverly, MA, USA", 
            "Pacific Biosciences, 94025, Adams Drive, Menlo Park, CA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Ranade", 
        "givenName": "Swati", 
        "id": "sg:person.01333000363.07", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01333000363.07"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Charles Street, 02141, Cambridge, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Shea", 
        "givenName": "Terrance P", 
        "id": "sg:person.011632400642.48", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011632400642.48"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Charles Street, 02141, Cambridge, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Williams", 
        "givenName": "Louise", 
        "id": "sg:person.01157521166.17", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01157521166.17"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Charles Street, 02141, Cambridge, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Young", 
        "givenName": "Sarah", 
        "id": "sg:person.0757557240.16", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0757557240.16"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Charles Street, 02141, Cambridge, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Nusbaum", 
        "givenName": "Chad", 
        "id": "sg:person.01170225154.35", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01170225154.35"
        ], 
        "type": "Person"
      }, 
      {
        "affiliation": {
          "alternateName": "Broad Institute", 
          "id": "https://www.grid.ac/institutes/grid.66859.34", 
          "name": [
            "Broad Institute of MIT and Harvard, Charles Street, 02141, Cambridge, MA, USA"
          ], 
          "type": "Organization"
        }, 
        "familyName": "Jaffe", 
        "givenName": "David B", 
        "id": "sg:person.01355660531.12", 
        "sameAs": [
          "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01355660531.12"
        ], 
        "type": "Person"
      }
    ], 
    "citation": [
      {
        "id": "https://doi.org/10.1101/gr.079053.108", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1005708074"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.171285098", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010138766"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1117389", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1010697532"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1111/j.1574-6968.2008.01441.x", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1016462719"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btl629", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017299791"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature02390", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017627596", 
          "https://doi.org/10.1038/nature02390"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature02390", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1017627596", 
          "https://doi.org/10.1038/nature02390"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.1270", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021189255", 
          "https://doi.org/10.1038/nmeth.1270"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature03959", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021574562", 
          "https://doi.org/10.1038/nature03959"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature03959", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1021574562", 
          "https://doi.org/10.1038/nature03959"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.1311", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1023653905", 
          "https://doi.org/10.1038/nmeth.1311"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature01554", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024199275", 
          "https://doi.org/10.1038/nature01554"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature01554", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1024199275", 
          "https://doi.org/10.1038/nature01554"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.7088808", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1025227180"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1150427", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1030422156"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.6435207", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1033023123"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.7337908", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1035219026"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1073/pnas.81.21.6812", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1037702115"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.072033.107", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038496028"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.8.3.186", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1038920266"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1093/bioinformatics/btm451", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051622036"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1101/gr.074492.107", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1051720574"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nmeth.1286", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052844738", 
          "https://doi.org/10.1038/nmeth.1286"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "sg:pub.10.1038/nature07517", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1052925719", 
          "https://doi.org/10.1038/nature07517"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.1071837", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062446551"
        ], 
        "type": "CreativeWork"
      }, 
      {
        "id": "https://doi.org/10.1126/science.311.5767.1544", 
        "sameAs": [
          "https://app.dimensions.ai/details/publication/pub.1062591532"
        ], 
        "type": "CreativeWork"
      }
    ], 
    "datePublished": "2009-10", 
    "datePublishedReg": "2009-10-01", 
    "description": "We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes of varied GC composition and sizes up to 40 Mb, ALLPATHS2 generated assemblies with long, accurate contigs and scaffolds. Velvet and EULER-SR were less accurate. For example, for Escherichia coli, the fraction of 10-kb stretches that were perfect was 99.8% (ALLPATHS2), 68.7% (Velvet), and 42.1% (EULER-SR).", 
    "genre": "research_article", 
    "id": "sg:pub.10.1186/gb-2009-10-10-r103", 
    "inLanguage": [
      "en"
    ], 
    "isAccessibleForFree": true, 
    "isPartOf": [
      {
        "id": "sg:journal.1023439", 
        "issn": [
          "1474-760X", 
          "1465-6906"
        ], 
        "name": "Genome Biology", 
        "type": "Periodical"
      }, 
      {
        "issueNumber": "10", 
        "type": "PublicationIssue"
      }, 
      {
        "type": "PublicationVolume", 
        "volumeNumber": "10"
      }
    ], 
    "name": "ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads", 
    "pagination": "r103", 
    "productId": [
      {
        "name": "readcube_id", 
        "type": "PropertyValue", 
        "value": [
          "3d000705ed30f21cd760269dc1e13979fca792119ffbba0c371d9e2875284ccf"
        ]
      }, 
      {
        "name": "pubmed_id", 
        "type": "PropertyValue", 
        "value": [
          "19796385"
        ]
      }, 
      {
        "name": "nlm_unique_id", 
        "type": "PropertyValue", 
        "value": [
          "100960660"
        ]
      }, 
      {
        "name": "doi", 
        "type": "PropertyValue", 
        "value": [
          "10.1186/gb-2009-10-10-r103"
        ]
      }, 
      {
        "name": "dimensions_id", 
        "type": "PropertyValue", 
        "value": [
          "pub.1012804464"
        ]
      }
    ], 
    "sameAs": [
      "https://doi.org/10.1186/gb-2009-10-10-r103", 
      "https://app.dimensions.ai/details/publication/pub.1012804464"
    ], 
    "sdDataset": "articles", 
    "sdDatePublished": "2019-04-11T00:15", 
    "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_8695_00000511.jsonl", 
    "type": "ScholarlyArticle", 
    "url": "http://link.springer.com/10.1186%2Fgb-2009-10-10-r103"
  }
]
 

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/gb-2009-10-10-r103'

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/gb-2009-10-10-r103'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1186/gb-2009-10-10-r103'

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

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1186/gb-2009-10-10-r103'


 

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

275 TRIPLES      21 PREDICATES      59 URIs      28 LITERALS      16 BLANK NODES

Subject Predicate Object
1 sg:pub.10.1186/gb-2009-10-10-r103 schema:about N0e06ac3a83b0460081a41c46d7fc1a19
2 N1616111efaf2411fb2b48177782b603b
3 N170c9e31a23f43b3b5792ce6e4423c44
4 N4d855cf1762c4a149e20f9e0c8ac35fb
5 N50065396d7df4914ac2a51e035c34f72
6 N5b7e37169b34456ea028a4d1b87b645b
7 N8e2389769d6449f88f6f03add91f5884
8 anzsrc-for:06
9 anzsrc-for:0605
10 schema:author N302a3e74574840d88afbd087db4283f5
11 schema:citation sg:pub.10.1038/nature01554
12 sg:pub.10.1038/nature02390
13 sg:pub.10.1038/nature03959
14 sg:pub.10.1038/nature07517
15 sg:pub.10.1038/nmeth.1270
16 sg:pub.10.1038/nmeth.1286
17 sg:pub.10.1038/nmeth.1311
18 https://doi.org/10.1073/pnas.171285098
19 https://doi.org/10.1073/pnas.81.21.6812
20 https://doi.org/10.1093/bioinformatics/btl629
21 https://doi.org/10.1093/bioinformatics/btm451
22 https://doi.org/10.1101/gr.072033.107
23 https://doi.org/10.1101/gr.074492.107
24 https://doi.org/10.1101/gr.079053.108
25 https://doi.org/10.1101/gr.6435207
26 https://doi.org/10.1101/gr.7088808
27 https://doi.org/10.1101/gr.7337908
28 https://doi.org/10.1101/gr.8.3.186
29 https://doi.org/10.1111/j.1574-6968.2008.01441.x
30 https://doi.org/10.1126/science.1071837
31 https://doi.org/10.1126/science.1117389
32 https://doi.org/10.1126/science.1150427
33 https://doi.org/10.1126/science.311.5767.1544
34 schema:datePublished 2009-10
35 schema:datePublishedReg 2009-10-01
36 schema:description We demonstrate that genome sequences approaching finished quality can be generated from short paired reads. Using 36 base (fragment) and 26 base (jumping) reads from five microbial genomes of varied GC composition and sizes up to 40 Mb, ALLPATHS2 generated assemblies with long, accurate contigs and scaffolds. Velvet and EULER-SR were less accurate. For example, for Escherichia coli, the fraction of 10-kb stretches that were perfect was 99.8% (ALLPATHS2), 68.7% (Velvet), and 42.1% (EULER-SR).
37 schema:genre research_article
38 schema:inLanguage en
39 schema:isAccessibleForFree true
40 schema:isPartOf N2d538559632c4c02809d9e304481589b
41 N75c49c7f955e4c64bcf0f159275212e4
42 sg:journal.1023439
43 schema:name ALLPATHS 2: small genomes assembled accurately and with high continuity from short paired reads
44 schema:pagination r103
45 schema:productId N020df8b9171842a29e5bf904f6b007f3
46 N6e0ca81c356849819bb08a457c894671
47 N81ea3c4c5696401b956228f18fb4d68b
48 Nef6694dd04194730bc95ac13631e7de9
49 Nfc9d950fd943475688ce06ff108eb316
50 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012804464
51 https://doi.org/10.1186/gb-2009-10-10-r103
52 schema:sdDatePublished 2019-04-11T00:15
53 schema:sdLicense https://scigraph.springernature.com/explorer/license/
54 schema:sdPublisher N8dde0c884c3c4e069f156a5748b0d352
55 schema:url http://link.springer.com/10.1186%2Fgb-2009-10-10-r103
56 sgo:license sg:explorer/license/
57 sgo:sdDataset articles
58 rdf:type schema:ScholarlyArticle
59 N020df8b9171842a29e5bf904f6b007f3 schema:name doi
60 schema:value 10.1186/gb-2009-10-10-r103
61 rdf:type schema:PropertyValue
62 N0e06ac3a83b0460081a41c46d7fc1a19 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
63 schema:name Genome
64 rdf:type schema:DefinedTerm
65 N1616111efaf2411fb2b48177782b603b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
66 schema:name Genomics
67 rdf:type schema:DefinedTerm
68 N170c9e31a23f43b3b5792ce6e4423c44 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
69 schema:name Reproducibility of Results
70 rdf:type schema:DefinedTerm
71 N25635625c170452785b496287f015798 rdf:first sg:person.01171316726.17
72 rdf:rest N7619f28b258543cda7bbbad0d9578cfb
73 N2d538559632c4c02809d9e304481589b schema:volumeNumber 10
74 rdf:type schema:PublicationVolume
75 N302a3e74574840d88afbd087db4283f5 rdf:first sg:person.01057437731.69
76 rdf:rest Nbda479f6207b494c8f43aefe36d77ce4
77 N4d855cf1762c4a149e20f9e0c8ac35fb schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
78 schema:name Bacteria
79 rdf:type schema:DefinedTerm
80 N50065396d7df4914ac2a51e035c34f72 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
81 schema:name Base Pairing
82 rdf:type schema:DefinedTerm
83 N5563a94416fd46e4a0989b0cd9a0039d rdf:first sg:person.01355660531.12
84 rdf:rest rdf:nil
85 N5b7e37169b34456ea028a4d1b87b645b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
86 schema:name Fungi
87 rdf:type schema:DefinedTerm
88 N67305852dc1e4cebaf6dc4e3e6cbaa59 rdf:first sg:person.011632400642.48
89 rdf:rest Nb922978bf8e24ed1bf850e8529a0045e
90 N6e0ca81c356849819bb08a457c894671 schema:name nlm_unique_id
91 schema:value 100960660
92 rdf:type schema:PropertyValue
93 N75c49c7f955e4c64bcf0f159275212e4 schema:issueNumber 10
94 rdf:type schema:PublicationIssue
95 N7619f28b258543cda7bbbad0d9578cfb rdf:first sg:person.0625052656.12
96 rdf:rest N83beb9804424425e8a9c78e9433e741b
97 N7fc838b099db4ef8b67ee1480e247ebe rdf:first sg:person.01333000363.07
98 rdf:rest N67305852dc1e4cebaf6dc4e3e6cbaa59
99 N81ea3c4c5696401b956228f18fb4d68b schema:name readcube_id
100 schema:value 3d000705ed30f21cd760269dc1e13979fca792119ffbba0c371d9e2875284ccf
101 rdf:type schema:PropertyValue
102 N83beb9804424425e8a9c78e9433e741b rdf:first sg:person.0645200471.91
103 rdf:rest Nb0555278d23a495cade322d0345f8c15
104 N8dde0c884c3c4e069f156a5748b0d352 schema:name Springer Nature - SN SciGraph project
105 rdf:type schema:Organization
106 N8e2389769d6449f88f6f03add91f5884 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
107 schema:name Software
108 rdf:type schema:DefinedTerm
109 Nac4c4beeec014949aabda09072dba4cb rdf:first sg:person.01170225154.35
110 rdf:rest N5563a94416fd46e4a0989b0cd9a0039d
111 Nb0555278d23a495cade322d0345f8c15 rdf:first sg:person.01252210540.25
112 rdf:rest Ne891ac4b94ac451ab627b512a27ca28e
113 Nb922978bf8e24ed1bf850e8529a0045e rdf:first sg:person.01157521166.17
114 rdf:rest Nc26e594c669648758bae4305b8ce302e
115 Nbda479f6207b494c8f43aefe36d77ce4 rdf:first sg:person.01127255432.56
116 rdf:rest Ne080087001594450acb03b5f65aa3f6e
117 Nc26e594c669648758bae4305b8ce302e rdf:first sg:person.0757557240.16
118 rdf:rest Nac4c4beeec014949aabda09072dba4cb
119 Ne080087001594450acb03b5f65aa3f6e rdf:first sg:person.0761567341.00
120 rdf:rest N25635625c170452785b496287f015798
121 Ne891ac4b94ac451ab627b512a27ca28e rdf:first sg:person.0614733731.46
122 rdf:rest N7fc838b099db4ef8b67ee1480e247ebe
123 Nef6694dd04194730bc95ac13631e7de9 schema:name dimensions_id
124 schema:value pub.1012804464
125 rdf:type schema:PropertyValue
126 Nfc9d950fd943475688ce06ff108eb316 schema:name pubmed_id
127 schema:value 19796385
128 rdf:type schema:PropertyValue
129 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
130 schema:name Biological Sciences
131 rdf:type schema:DefinedTerm
132 anzsrc-for:0605 schema:inDefinedTermSet anzsrc-for:
133 schema:name Microbiology
134 rdf:type schema:DefinedTerm
135 sg:journal.1023439 schema:issn 1465-6906
136 1474-760X
137 schema:name Genome Biology
138 rdf:type schema:Periodical
139 sg:person.01057437731.69 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
140 schema:familyName MacCallum
141 schema:givenName Iain
142 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01057437731.69
143 rdf:type schema:Person
144 sg:person.01127255432.56 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
145 schema:familyName Przybylski
146 schema:givenName Dariusz
147 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01127255432.56
148 rdf:type schema:Person
149 sg:person.01157521166.17 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
150 schema:familyName Williams
151 schema:givenName Louise
152 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01157521166.17
153 rdf:type schema:Person
154 sg:person.011632400642.48 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
155 schema:familyName Shea
156 schema:givenName Terrance P
157 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011632400642.48
158 rdf:type schema:Person
159 sg:person.01170225154.35 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
160 schema:familyName Nusbaum
161 schema:givenName Chad
162 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01170225154.35
163 rdf:type schema:Person
164 sg:person.01171316726.17 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
165 schema:familyName Burton
166 schema:givenName Joshua
167 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01171316726.17
168 rdf:type schema:Person
169 sg:person.01252210540.25 schema:affiliation https://www.grid.ac/institutes/grid.416973.e
170 schema:familyName Malek
171 schema:givenName Joel
172 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01252210540.25
173 rdf:type schema:Person
174 sg:person.01333000363.07 schema:affiliation https://www.grid.ac/institutes/grid.423340.2
175 schema:familyName Ranade
176 schema:givenName Swati
177 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01333000363.07
178 rdf:type schema:Person
179 sg:person.01355660531.12 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
180 schema:familyName Jaffe
181 schema:givenName David B
182 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01355660531.12
183 rdf:type schema:Person
184 sg:person.0614733731.46 schema:affiliation https://www.grid.ac/institutes/grid.418190.5
185 schema:familyName McKernan
186 schema:givenName Kevin
187 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0614733731.46
188 rdf:type schema:Person
189 sg:person.0625052656.12 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
190 schema:familyName Shlyakhter
191 schema:givenName Ilya
192 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0625052656.12
193 rdf:type schema:Person
194 sg:person.0645200471.91 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
195 schema:familyName Gnirke
196 schema:givenName Andreas
197 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0645200471.91
198 rdf:type schema:Person
199 sg:person.0757557240.16 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
200 schema:familyName Young
201 schema:givenName Sarah
202 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0757557240.16
203 rdf:type schema:Person
204 sg:person.0761567341.00 schema:affiliation https://www.grid.ac/institutes/grid.66859.34
205 schema:familyName Gnerre
206 schema:givenName Sante
207 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0761567341.00
208 rdf:type schema:Person
209 sg:pub.10.1038/nature01554 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024199275
210 https://doi.org/10.1038/nature01554
211 rdf:type schema:CreativeWork
212 sg:pub.10.1038/nature02390 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017627596
213 https://doi.org/10.1038/nature02390
214 rdf:type schema:CreativeWork
215 sg:pub.10.1038/nature03959 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021574562
216 https://doi.org/10.1038/nature03959
217 rdf:type schema:CreativeWork
218 sg:pub.10.1038/nature07517 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052925719
219 https://doi.org/10.1038/nature07517
220 rdf:type schema:CreativeWork
221 sg:pub.10.1038/nmeth.1270 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021189255
222 https://doi.org/10.1038/nmeth.1270
223 rdf:type schema:CreativeWork
224 sg:pub.10.1038/nmeth.1286 schema:sameAs https://app.dimensions.ai/details/publication/pub.1052844738
225 https://doi.org/10.1038/nmeth.1286
226 rdf:type schema:CreativeWork
227 sg:pub.10.1038/nmeth.1311 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023653905
228 https://doi.org/10.1038/nmeth.1311
229 rdf:type schema:CreativeWork
230 https://doi.org/10.1073/pnas.171285098 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010138766
231 rdf:type schema:CreativeWork
232 https://doi.org/10.1073/pnas.81.21.6812 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037702115
233 rdf:type schema:CreativeWork
234 https://doi.org/10.1093/bioinformatics/btl629 schema:sameAs https://app.dimensions.ai/details/publication/pub.1017299791
235 rdf:type schema:CreativeWork
236 https://doi.org/10.1093/bioinformatics/btm451 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051622036
237 rdf:type schema:CreativeWork
238 https://doi.org/10.1101/gr.072033.107 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038496028
239 rdf:type schema:CreativeWork
240 https://doi.org/10.1101/gr.074492.107 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051720574
241 rdf:type schema:CreativeWork
242 https://doi.org/10.1101/gr.079053.108 schema:sameAs https://app.dimensions.ai/details/publication/pub.1005708074
243 rdf:type schema:CreativeWork
244 https://doi.org/10.1101/gr.6435207 schema:sameAs https://app.dimensions.ai/details/publication/pub.1033023123
245 rdf:type schema:CreativeWork
246 https://doi.org/10.1101/gr.7088808 schema:sameAs https://app.dimensions.ai/details/publication/pub.1025227180
247 rdf:type schema:CreativeWork
248 https://doi.org/10.1101/gr.7337908 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035219026
249 rdf:type schema:CreativeWork
250 https://doi.org/10.1101/gr.8.3.186 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038920266
251 rdf:type schema:CreativeWork
252 https://doi.org/10.1111/j.1574-6968.2008.01441.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1016462719
253 rdf:type schema:CreativeWork
254 https://doi.org/10.1126/science.1071837 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062446551
255 rdf:type schema:CreativeWork
256 https://doi.org/10.1126/science.1117389 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010697532
257 rdf:type schema:CreativeWork
258 https://doi.org/10.1126/science.1150427 schema:sameAs https://app.dimensions.ai/details/publication/pub.1030422156
259 rdf:type schema:CreativeWork
260 https://doi.org/10.1126/science.311.5767.1544 schema:sameAs https://app.dimensions.ai/details/publication/pub.1062591532
261 rdf:type schema:CreativeWork
262 https://www.grid.ac/institutes/grid.416973.e schema:alternateName Weill Cornell Medical College in Qatar
263 schema:name Department of Medical Genetics, Weill Cornell Medical College in Qatar, Al-Rayaan St., 24144, Doha, Qatar
264 Life Technologies, Cummings Center, 01915, Beverly, MA, USA
265 rdf:type schema:Organization
266 https://www.grid.ac/institutes/grid.418190.5 schema:alternateName Thermo Fisher Scientific (United States)
267 schema:name Life Technologies, Cummings Center, 01915, Beverly, MA, USA
268 rdf:type schema:Organization
269 https://www.grid.ac/institutes/grid.423340.2 schema:alternateName Pacific Biosciences (United States)
270 schema:name Life Technologies, Cummings Center, 01915, Beverly, MA, USA
271 Pacific Biosciences, 94025, Adams Drive, Menlo Park, CA, USA
272 rdf:type schema:Organization
273 https://www.grid.ac/institutes/grid.66859.34 schema:alternateName Broad Institute
274 schema:name Broad Institute of MIT and Harvard, Charles Street, 02141, Cambridge, MA, USA
275 rdf:type schema:Organization
 




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


...