Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in...
Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank
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England: BioMed Central Ltd
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English
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England: BioMed Central Ltd
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Genomic analyses are sensitive to contamination in public databases caused by incorrectly labeled reference sequences. Here, we describe Conterminator, an efficient method to detect and remove incorrectly labeled sequences by an exhaustive all-against-all sequence comparison. Our analysis reports contamination of 2,161,746, 114,035, and 14,148 sequences in the RefSeq, GenBank, and NR databases, respectively, spanning the whole range from draft to “complete” model organism genomes. Our method scales linearly with input size and can process 3.3 TB in 12 days on a 32-core computer. Conterminator can help ensure the quality of reference databases. Source code (GPLv3):
https://github.com/martin-steinegger/conterminator...
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Full title
Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank
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TN_cdi_doaj_primary_oai_doaj_org_article_0c58db75fd8a487eb02d1ef019ea16a4
Permalink
https://devfeature-collection.sl.nsw.gov.au/record/TN_cdi_doaj_primary_oai_doaj_org_article_0c58db75fd8a487eb02d1ef019ea16a4
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ISSN
1474-760X,1474-7596
E-ISSN
1474-760X
DOI
10.1186/s13059-020-02023-1
