Malte B. Hallgren
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View article: Assembly-free typing of Nanopore and Illumina data through proximity scoring with KMA
Assembly-free typing of Nanopore and Illumina data through proximity scoring with KMA Open
Advances in Oxford Nanopore Technologies (ONT) with the introduction of the r10.4.1 flow cell have reduced the sequencing error rates to <1%. When a reference sequence is known, this allows for accurate variant calling comparable with what…
NanoMGT: Marker gene typing of low complexity mono-species metagenomic samples using noisy long reads Open
Rapid advancements in sequencing technologies have led to significant progress in microbial genomics, yet challenges persist in accurately identifying microbial strain diversity in metagenomic samples, especially when working with noisy lo…
Nanopore sequencing technology for clinical diagnosis of infectious diseases where laboratory capacity is meager: A case report Open
In resource-limited settings, patients are often first presented to clinical settings when seriously ill and access to proper clinical microbial diagnostics is often very limited or non-existing. On February 16th, 2022 we were on a field t…
MINTyper: An outbreak-detection method for accurate and rapid SNP typing of clonal clusters with noisy long reads Open
For detection of clonal outbreaks in clinical settings, we present a complete pipeline that generates a SNP-distance matrix from a set of sequencing reads. Importantly, the program is able to handle a separate mix of both short reads from …