SNIT: SNP identification for strain typing
SNP identification for strain typing (SNIT)

SNIT is a simple, fast pipeline to compare a set of bacterial genomes to identify the nearest neighbor for each input genome. The SNIT pipeline can be used to rapidly identify the closest neighbor of a newly sequenced bacterial genome based on the numbers of shared polymorphisms with previously known genomes of the same species. SNIT uses MUMmer [1] to perform pairwise alignments between the genomes.

      

The SNIT pipeline has many advantages: (1) it is a stand-alone application with a graphical interface that is easy to install on the user’s workstation, thus avoiding any problems with uploading or sharing the sequences; (2) it is fast and highly scalable due to the basic functionality of SNP finding based on pairwise alignments; and (3) it identifies the closest neighbor for each genome with high accuracy without the necessity for further processing of the SNP data by the user.

The SNP identification modules from SNIT have been incorporated into TOFI [2-4] and TOPSI [5] pipelines for designing pathogen diagnostic assays with strain-specific signatures.

[1]Kurtz, S., A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, C. Antonescu, and S.L. Salzberg, Versatile and open software for comparing large genomes. Genome Biol, 2004. 5(2): p. R12.
[2]Tembe, W., N. Zavaljevski, E. Bode, C. Chase, J. Geyer, L. Wasieloski, G. Benson, and J. Reifman, Oligonucleotide fingerprint identification for microarray-based pathogen diagnostic assays. Bioinformatics, 2007. 23(1): p. 5-13.
[3]Vijaya Satya, R., N. Zavaljevski, K. Kumar, E. Bode, S. Padilla, L. Wasieloski, J. Geyer, and J. Reifman, In silico microarray probe design for diagnosis of multiple pathogens. BMC Genomics, 2008. 9(1): p. 496.
[4]Vijaya Satya, R., N. Zavaljevski, K. Kumar, and J. Reifman, A high-throughput pipeline for designing microarray-based pathogen diagnostic assays. BMC Bioinformatics, 2008. 9(1): p. 185.
[5]Vijaya Satya, R., K. Kumar, N. Zavaljevski, and J. Reifman, A high-throughput pipeline for the design of real-time PCR signatures. BMC Bioinformatics, 2010. 11: p. 340.
Resources
  • SNIT Manual [PDF]
  • Download SNIT distribution [gzip]
Publications
Vijaya Satya R., Zavaljevski N., and Reifman J. SNIT: SNP identification for strain typing. In preparation.