SNIT: A Tool for Identifying Bacterial Strains
Author Information
Author(s): Vijaya Satya Ravi, Zavaljevski Nela, Reifman Jaques
Primary Institution: Biotechnology HPC Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Materiel Command
Hypothesis
The SNIT pipeline can accurately identify single nucleotide polymorphisms (SNPs) and small indels for strain typing of bacterial genomes.
Conclusion
The SNIT pipeline accurately identifies the closest bacterial neighbors with 75% to 100% accuracy across different species.
Supporting Evidence
- The SNIT pipeline took less than 2 minutes to compare four S. flexneri genomes.
- The pipeline achieved 100% accuracy for four out of five bacterial species tested.
- For Burkholderia pseudomallei, the accuracy was 75%, indicating challenges with highly divergent strains.
Takeaway
The SNIT tool helps scientists quickly find out which bacteria are most similar to a newly sequenced one by looking at tiny differences in their DNA.
Methodology
The SNIT pipeline uses pairwise alignments to identify SNPs and small indels by comparing a newly sequenced genome with other genomes of the same species.
Potential Biases
The reliance on reference genomes may introduce bias in SNP reporting.
Limitations
The pipeline may not perform well with highly divergent species or those with significant horizontal gene transfer.
Digital Object Identifier (DOI)
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