Key message
Panfeed, a newly developed python-based command line tool, addresses limitations in bacterial genome-wide association studies by linking k-mers to specific gene clusters, circumventing common confounding factors of de Bruijn graph based methods when identifying causal variants within microbial datasets.
Translationale Perspektive
Panfeed reduces the ambiguity of GWAS by facilitating the association between gene cluster specific mutations, especially in promoter regions, and phenotype alterations, thereby fostering a more comprehensive understanding of microbial pathogen strategies and enabling the exploration of novel antimicrobial targets.
Original publication
Hannes Sommer, Dilfuza Djamalova, Marco Galardini
Reduced ambiguity and improved interpretability of bacterial genome-wide associations using gene-cluster-centric k-mers
Microbial Genomics, 2023