ConFindr: rapid detection of intraspecies and cross-species contamination in bacterial whole-genome sequence data.

ABSTRACT: Whole-genome sequencing (WGS) of bacterial pathogens is currently widely used to support public-health investigations. The ability to assess WGS data quality is critical to underpin the reliability of downstream analyses. Sequence contamination is a quality issue that could potentially impact WGS-based findings; however, existing tools do not readily identify contamination from closely-related organisms. To address this gap, we have developed a computational pipeline, ConFindr, for detection of intraspecies contamination. ConFindr determines the presence of contaminating sequences based on the identification of multiple alleles of core, single-copy, ribosomal-protein genes in raw sequencing reads. The performance of this tool was assessed using simulated and lab-generated Illumina short-re

SUBMITTER: Low AJ 

PROVIDER: S-EPMC6546082 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature