Samantha A W Crouch, Jan Krause, Thomas Dandekar, Tim Breitenbach
DataXflow: Synergizing data-driven modeling with best parameter fit and optimal control - An efficient data analysis for cancer research
Computational and structural biotechnology journal
metagenomic sequencing promising method potential revolutionize world pathogen detection antimicrobial resistance amr surveillance foodproducing environments however analysis huge amount data obtained requires performant bioinformatics tools databases intuitive straightforward interpretation study based longread metagenomics data chicken fecal samples spikein mock community proposed confidence levels taxonomic identification amr gene detection interpretation guidelines help analysis output data generated kma popular kmer read alignment tool additionally demonstrated completeness diversity genomes present reference databases key parameters accurate easy interpretation sequencing data finally explored whether kma twostep procedure used link detected amr genes bacterial host chromosome detected within longreads confidence levels successfully tested 28 metagenomics datasets obtained sequencing real spiked samples fecal chicken pig buffalo food minced beef food enzyme products origin methodology proposed study facilitate analysis metagenomics sequencing datasets kma users ultimately contribute improvements rapid diagnosis surveillance pathogens amr genes foodproducing environments prioritized eu