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ahmedmagds / GNUVID:GNUVID v2.0:截至2020-10-20的全球流通的克隆复合体

艾哈迈德·穆斯塔法


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{
  "publisher": "Zenodo", 
  "DOI": "10.5281 / zenodo.4313855", 
  "title": "ahmedmagds / GNUVID:GNUVID v2.0:截至2020-10-20的全球流通的克隆复合体", 
  "issued": {
    "date-parts": [
      [
        2020, 
        12, 
        9
      ]
    ]
  }, 
  "abstract": "<p>GNUVID 2.0</p>\nBig update\n<p>This release of GNUVID comes with a significant speed-up and improved classification. The new classification algorithm is called GNUVID_Predict.</p>\n<p>Use of GNUVID now is as simple as GNUVID query_fasta.fna</p>\n<p>As of GNUVID 2.0, GNUVID_Predict.py is a speedy algorithm for assigning Clonal Complexes to new genomes, which uses a Machine Learning Random Forest Classifier.</p>\n<p>The model was trained using 53,565 SARS-CoV-2 sequences from GISAID. The alignment of these genomes to MN908947.3 was one-hot encoded. The Classifier model was built using the sci-kit learn implementation of Random Forest.</p>\nGlobally circulating clonal complexes as  of 2020-10-20:\n<ul>\n<li><p>69686 GISAID sequences have been included in this analysis.</p>\n</li>\n<li><p>GNUVID compressed the 696860 ORFs in the 69686 genomes to 37921 unique alleles.</p>\n</li>\n<li><p>35010 Sequence Types (STs) have been assigned in this dataset and were clustered in 154 clonal complexes (CCs).</p>\n</li>\n<li><p>84 new CCs have been assigned.</p>\n</li>\n<li><p>82 CCs have been Inactive (i.e. Last time seen more than 1 month before 2020-10-20).</p>\n</li>\n<li><p>27 CCs have gone Quiet (i.e. Last seen 2-4 weeks before 2020-10-20).</p>\n</li>\n<li><p>45 CCs have been Active (i.e. Last seen within the 2 weeks before 2020-10-20).</p>\n</li>\n<li><p>CC70, CC26, CC343, CC439, CC927, CC1434, CC11290, CC13202, CC13669 and CC17244 have now been called CC550, CC750, CC9999, CC2649, CC1179, CC2175, CC18372, CC13208, CC12995 and CC13413 respectively.</p>\n</li>\n</ul>", 
  "author": [
    {
      "family": "Ahmed M Moustafa"
    }
  ], 
  "version": "v2.0", 
  "type": "article", 
  "id": "4313855"
}
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