Comparative analysis of metagenomic classifiers for long-read sequencing datasets.

ABSTRACT:

Background

Long reads have gained popularity in the analysis of metagenomics data. Therefore, we comprehensively assessed metagenomics classification tools on the species taxonomic level. We analysed kmer-based tools, mapping-based tools and two general-purpose long reads mappers. We evaluated more than 20 pipelines which use either nucleotide or protein databases and selected 13 for an extensive benchmark. We prepared seven synthetic datasets to test various scenarios, including the presence of a host, unknown species and related species. Moreover, we used available sequencing data from three well-defined mock communities, including a dataset with abundance varying from 0.0001 to 20% and six real gut microbiomes.

Results

General-purpose mappers Minimap2 and Ram achieved sim

SUBMITTER: Maric J 

PROVIDER: S-EPMC10782538 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature