A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics

• DOI: 10.1128/spectrum.03590-23
• Publication Date: 2024-03-07T15:26:21Z
• Authors: Raphael Eisenhofer; Joseph Nesme; Luisa Santos-Bay; Adam Koziol; Søren Johannes Sø...; Antton Alberdi; Ostaizka Aizpurua
• Keywords: Sequence assembly; Hybrid genome assembly

ABSTRACT Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well combination both. To assess pros cons these different approaches, we used 22 fecal DNA extracts collected weekly for 11 weeks from two respective lab mice to study seven performance metrics over four combinations depth technology: (i) 20 Gbp Illumina (ii) 40 (iii) PacBio HiFi (iv) hybrid (20 +20 long-read) data. No strategy was best all metrics; instead, each one excelled across metrics. The yielded assembly statistics, with highest N50 lowest number contigs. refined bins. Finally, longest assemblies mapping rate bacterial genomes. Our results suggest that while significantly improves quality reconstructed genomes, it is more expensive requires deeper than approaches recover comparable amount most optimal study-specific depends on how researchers trade-off between quantity recovered IMPORTANCE Mice are important model organism understanding gut microbiome. When studying microbiomes techniques, choose technologies use short or long reads. In this study, perform extensive benchmark short- microbiomes. We find no provide information help guide in planning their experiments.