Ultra-fast and cost-effective pathogen identification and resistance gene detection in a clinical research setting using nanopore Flongle sequencing
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Flongle sequencing can be successfully used for the identification of bacteria and AMR in clinical isolates and as well as spiked blood samples. Using one flow cell per sample provide the most relevant information. Sequencing can be stopped after the first 20,000-50,000 sequences (genome covered once). Flongle showed error in ARG variant calling but was similar to MinION in real-time pathogen ID and AMR.