November 22, 2022

Evaluation of taxonomic profiling methods for long-read shotgun metagenomic sequencing datasets

Author(s): Portik, Daniel M. and Wilkinson, Jeremy E and Brown, C. Titus and Pierce-Ward, N. Tessa

Long-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher information content in long reads is useful for taxonomic profiling, where the main goal is to identify the species present in a microbiome sample (typically bacteria, archaea, fungi, viruses) and their relative abundances. The development of long-read specific tools for taxonomic profiling is accelerating, yet there is a lack of consensus regarding their relative performance. We performed a critical benchmarking study using five long-read methods and four popular short-read methods1. We applied these tools to several mock community datasets generated using PacBio HiFi sequencing or Oxford Nanopore Technology (ONT) sequencing, and Illumina data.

Organization: PacBio
Year: 2022

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