CoDing Sequence Typer (CDST): a fast, simple, decentralized and interoperable solution for bacterial genomic typing and clustering.

ABSTRACT: We present a fully decentralized MD5 hash-based framework that indexes predicted coding sequences (CDSs) and computes pairwise genomic distances without locus annotation or a central database. The method is implemented in the open-source CoDing Sequence Typer (CDST) pipeline, which delivers reproducible, privacy-preserving and computationally efficient bacterial typing. Applied to 1,961 complete Salmonella enterica genomes, CDST produced distance matrices that were highly concordant with core-genome multilocus sequence typing (cgMLST) and whole-genome MLST (wgMLST), core-genome SNP, Mash and Split Kmer analysis. In a 100-genome benchmark, CDST achieved ~8× faster runtimes than cg/wgMLST workflows and reduced storage to ~4% of the original assembly FASTA size. Unsupervised clustering

SUBMITTER: Li M 

PROVIDER: S-EPMC12548756 | biostudies-literature | 2025 Oct

REPOSITORIES: biostudies-literature