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SNIT: SNP identification for strain typing by Ravi Vijaya Satya; Nela Zavaljevski; Jaques Reifman is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

What is SNIT: SNP identification for strain typing about?

With ever-increasing numbers of microbial genomes being sequenced, efficient tools are needed to perform strain-level identification of any newly sequenced genome. Here, we present the SNP identification for strain typing (SNIT) pipeline, a fast and accurate software system that compares a newly sequenced bacterial genome with other genomes of the same species to identify single nucleotide polymorphisms (SNPs) and small insertions/deletions (indels). Based on this information, the pipeline analyzes the polymorphic loci present in all input genomes to identify the genome that has the fewest differences with the newly sequenced genome. Similarly, for each of the other genomes, SNIT identifies the input genome with the fewest differences. Results from five bacterial species show that the SNIT pipeline identifies the correct closest neighbor with 75% to 100% accuracy. The SNIT pipeline is available for download at http://www.bhsai.org/snit.html

Who reads SNIT: SNP identification for strain typing?

Author

Ravi Vijaya Satya; Nela Zavaljevski; Jaques Reifman

Publisher

BioMed Central; Springer (Biomed Central Ltd.); [London]: BioMed Central, 2006-; Springer Science and Business Media LLC (ISSN 1751-0473)

Published

2011

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)