Terminating contamination: Large-scale search identifies more than 2,000,000 contaminated entries in GenBank

Martin Steinegger, Steven L. Salzberg

Research output: Contribution to journalArticlepeer-review

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

Original languageEnglish (US)
Article number115
JournalGenome biology
Volume21
Issue number1
DOIs
StatePublished - May 12 2020

Keywords

  • Contamination
  • GenBank
  • Genomes
  • RefSeq
  • Software

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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