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• W2953115170 abstract "Background Fast, accurate and high-throughput detection of bacteria is in great demand. The present work was conducted to investigate the possibility of identifying both known and unknown bacterial strains from unassembled next-generation sequencing reads using custom-made guide trees. Results A program named StrainSeeker was developed that constructs a list of specific k-mers for each node of any given Newick-format tree and enables rapid identification of bacterial genomes within minutes. StrainSeeker has been tested and shown to successfully identify Escherichia coli strains from mixed samples in less than 5 minutes. StrainSeeker can also identify bacterial strains from highly diverse metagenomics samples. StrainSeeker is available at http://bioinfo.ut.ee/strainseeker. Conclusions Our novel approach can be useful for both clinical diagnostics and research laboratories because novel bacterial strains are constantly emerging and their fast and accurate detection is very important." @default.
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• W2953115170 date "2016-02-19" @default.
• W2953115170 modified "2023-10-16" @default.
• W2953115170 title "StrainSeeker: fast identification of bacterial strains from unassembled sequencing reads using user-provided guide trees." @default.
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• W2953115170 doi "https://doi.org/10.1101/040261" @default.
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