Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes.

ABSTRACT: Recent technological and computational advances have made metagenomic assembly a viable approach to achieving high-resolution views of complex microbial communities. In previous benchmarking, short-read (SR) metagenomic assemblers had the highest accuracy, long-read (LR) assemblers generated the most contiguous sequences and hybrid (HY) assemblers balanced length and accuracy. However, no assessments have specifically compared the performance of these assemblers on low-abundance species, which include clinically relevant organisms in the gut. We generated semi-synthetic LR and SR datasets by spiking small and increasing amounts of Escherichia coli isolate reads into fecal metagenomes and, using different assemblers, examined E. coli contigs and the presence of antibiotic resistance genes (

SUBMITTER: Yorki S 

PROVIDER: S-EPMC10025444 | biostudies-literature | 2023 Mar

REPOSITORIES: biostudies-literature