Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank
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 r...
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| Format: | Article |
| Language: | English |
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BMC
2020-05-01
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| Series: | Genome Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s13059-020-02023-1 |
| _version_ | 1819077772998344704 |
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| author | Martin Steinegger Steven L. Salzberg |
| author_facet | Martin Steinegger Steven L. Salzberg |
| author_sort | Martin Steinegger |
| collection | DOAJ |
| 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 |
| first_indexed | 2024-12-21T19:02:31Z |
| format | Article |
| id | doaj.art-0c58db75fd8a487eb02d1ef019ea16a4 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-21T19:02:31Z |
| publishDate | 2020-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-0c58db75fd8a487eb02d1ef019ea16a42022-12-21T18:53:27ZengBMCGenome Biology1474-760X2020-05-0121111210.1186/s13059-020-02023-1Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBankMartin Steinegger0Steven L. Salzberg1School of Biological Sciences, Seoul National UniversityCenter for Computational Biology, Whiting School of Engineering, Johns Hopkins UniversityAbstract 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/conterminatorhttp://link.springer.com/article/10.1186/s13059-020-02023-1GenomesContaminationSoftwareRefSeqGenBank |
| spellingShingle | Martin Steinegger Steven L. Salzberg Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank Genome Biology Genomes Contamination Software RefSeq GenBank |
| title | Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank |
| title_full | Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank |
| title_fullStr | Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank |
| title_full_unstemmed | Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank |
| title_short | Terminating contamination: large-scale search identifies more than 2,000,000 contaminated entries in GenBank |
| title_sort | terminating contamination large scale search identifies more than 2 000 000 contaminated entries in genbank |
| topic | Genomes Contamination Software RefSeq GenBank |
| url | http://link.springer.com/article/10.1186/s13059-020-02023-1 |
| work_keys_str_mv | AT martinsteinegger terminatingcontaminationlargescalesearchidentifiesmorethan2000000contaminatedentriesingenbank AT stevenlsalzberg terminatingcontaminationlargescalesearchidentifiesmorethan2000000contaminatedentriesingenbank |