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

作者：Martin Steinegger, Steven L. Salzberg · 发表于：Genome biology · 年份：2020 · DOI：10.1186/s13059-020-02023-1 · 被引用次数：271 · 研究领域：Genomics and Phylogenetic Studies、Environmental DNA in Biodiversity Studies、Microbial Community Ecology and Physiology

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.