MLVAType

MLVAType is a software tool that extracts multiple-locus variable numbers of tandem repeats (MLVA) profiles of Vibrio cholerae isolates from whole genome sequencing (WGS) data. It ensures backward compatibility with traditional MLVA typing methods, allowing users to compare MLVA profiles identified by WGS or conventional methods.

Validation tests comparing MLVAType results with Sanger sequencing and an in silico PCR approach showed complete concordance between them. However, MLVAType estimations were affected by censored results, which were inversely proportional to the k-mer parameter used during genome assembly.

Using a more extended k-mer size (e.g., 175) prevented censored estimation, but this option is not available in the current version of the SPAdes software. As NGS read lengths and qualities improve, it is expected that longer k-mer sizes will be available, enabling MLVAType to efficiently retrieve MLVA profiles from WGS data while avoiding censored estimation.