Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data.

ABSTRACT:

Background

Culture-free real-time sequencing of clinical metagenomic samples promises both rapid pathogen detection and antimicrobial resistance profiling. However, this approach introduces the risk of patient DNA leakage. To mitigate this risk, we need near-comprehensive removal of human DNA sequences at the point of sequencing, typically involving the use of resource-constrained devices. Existing benchmarks have largely focused on the use of standardized databases and largely ignored the computational requirements of depletion pipelines as well as the impact of human genome diversity.

Results

We benchmarked host removal pipelines on simulated and artificial real Illumina and Nanopore metagenomic samples. We found that construction of a custom kraken database containing div

SUBMITTER: Hall MB 

PROVIDER: S-EPMC10993716 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature