SeqSero2

SeqSero2 predicts Salmonella serotypes from whole-genome sequencing (WGS) data to enable rapid and accurate determination of species, subspecies, and serotype determinants for surveillance and research.

Key Features:

• k-mer based algorithm: Uses a k-mer based approach to enable rapid serotype prediction directly from raw sequencing reads, achieving processing times of seconds per genome and up to a 50-fold speed increase over the original SeqSero while maintaining equivalent accuracy for raw reads.
• Improved accuracy on assemblies: Enhances serotype prediction accuracy from draft genome assemblies via additional sequence markers that support identification of Salmonella species, subspecies, and specific serotypes.
• Targeted assembly: Employs targeted assembly methods to retrieve serotype determinants, supporting precise serotype prediction, new allele discovery, and troubleshooting of predictions.
• Contamination detection: Demonstrated contamination detection capability in testing on 5,794 genomes representing 364 common U.S. serotypes by identifying genomes containing reads from multiple serotypes (3% of tested cases).
• Compatibility with long reads: Supports long nanopore reads and showed accurate and rapid serotype prediction on nanopore data (40 tested genomes) with a single H antigen misidentification, indicating robustness to base call errors.

Scientific Applications:

• Public health surveillance: Supports whole-genome sequencing–based surveillance workflows for Salmonella serotype monitoring in public health and food safety laboratories.
• Integration with classic serotyping: Enables continuation of classic serotyping schemes by deriving serotype information from genomic data.
• Epidemiology and AMR studies: Applies to large-scale epidemiological investigations and antimicrobial resistance tracking by providing serotype-level resolution from short- and long-read data.

Methodology:

Analyzes WGS data using a k-mer based approach combined with targeted assembly techniques; upon execution results are written to a directory named 'SeqSero_result_Time_your_run' with detailed output in 'SeqSero_result.txt', and assembled alleles can be accessed when using the "-m a" (allele mode) option.