Journal
MICROBIAL GENOMICS
Volume 5, Issue 5, Pages -Publisher
MICROBIOLOGY SOC
DOI: 10.1099/mgen.0.000261
Keywords
SNP calling; bacterial comparative genomics; molecular epidemiology; benchmark; whole genome sequencing
Categories
Funding
- Japan Society for the Promotion of Science KAKENHI [15H05979, 16H04719, 16H05190, 16H06279, 18K19286]
- Grants-in-Aid for Scientific Research [16H04719, 15H05979, 16H05190, 18K19286] Funding Source: KAKEN
Ask authors/readers for more resources
Bacteria are highly diverse, even within a species; thus, there have been many studies which classify a single species into multiple types and analyze the genetic differences between them. Recently, the use of whole-genome sequencing (WGS) has been popular for these analyses, and the identification of single-nucleotide polymorphisms (SNPs) between isolates is the most basic analysis performed following WGS. The performance of SNP-calling methods therefore has a significant effect on the accuracy of downstream analyses, such as phylogenetic tree inference. In particular, when closely related isolates are analyzed, e.g. in outbreak investigations, some SNP callers tend to detect a high number of false-positive SNPs compared with the limited number of true SNPs among isolates. However, the performances of various SNP callers in such a situation have not been validated sufficiently. Here, we show the results of realistic benchmarks of commonly used SNP callers, revealing that some of them exhibit markedly low accuracy when target isolates are closely related. As an alternative, we developed a novel pipeline BactSNP, which utilizes both assembly and mapping information and is capable of highly accurate and sensitive SNP calling in a single step. BactSNP is also able to call SNPs among isolates when the reference genome is a draft one or even when the user does not input the reference genome. BactSNP is available at https://github.com/IEkAdN/BactSNP.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available