Accession Number:

ADA571154

Title:

SNIT: SNP Identification for Strain Typing

Descriptive Note:

Journal article

Corporate Author:

ARMY MEDICAL RESEARCH AND MATERIEL COMMAND FORT DETRICK MD TELEMEDICINE AND ADVANCED TECH RESEARCH CENTER

Report Date:

2011-01-01

Pagination or Media Count:

6.0

Abstract:

With ever-increasing numbers of microbial genomes being sequenced, efficient tools are needed to perform strainlevel 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 httpwww.bhsai.orgsnit.html

Subject Categories:

  • Biochemistry
  • Medicine and Medical Research

Distribution Statement:

APPROVED FOR PUBLIC RELEASE