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Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Steinegger, Martin | - |
dc.contributor.author | Salzberg, Steven L | - |
dc.date.accessioned | 2020-09-04T00:06:41Z | - |
dc.date.available | 2020-09-04T00:06:41Z | - |
dc.date.issued | 2020-05-12 | - |
dc.identifier.citation | Genome Biology, 21(1):115 | ko_KR |
dc.identifier.uri | https://hdl.handle.net/10371/168791 | - |
dc.description.abstract | 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 | ko_KR |
dc.description.sponsorship | This work was supported in part by NIH grants R35-GM130151 and R01-HG006677, and by NSF grant IOS-1744309 to SLS. | ko_KR |
dc.language.iso | en | ko_KR |
dc.publisher | BMC | ko_KR |
dc.subject | Genomes | - |
dc.subject | Contamination | - |
dc.subject | Software | - |
dc.subject | RefSeq | - |
dc.subject | GenBank | - |
dc.title | Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank | ko_KR |
dc.type | Article | ko_KR |
dc.identifier.doi | 10.1186/s13059-020-02023-1 | - |
dc.language.rfc3066 | en | - |
dc.rights.holder | The Author(s) | - |
dc.date.updated | 2020-06-17T13:16:52Z | - |
dc.citation.number | 1 | ko_KR |
dc.citation.startpage | 115 | ko_KR |
dc.citation.volume | 21 | ko_KR |
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