Swapping Metagenomics Preprocessing Pipeline Components Offers Speed and Sensitivity Increases.

ABSTRACT: Increasing data volumes on high-throughput sequencing instruments such as the NovaSeq 6000 leads to long computational bottlenecks for common metagenomics data preprocessing tasks such as adaptor and primer trimming and host removal. Here, we test whether faster recently developed computational tools (Fastp and Minimap2) can replace widely used choices (Atropos and Bowtie2), obtaining dramatic accelerations with additional sensitivity and minimal loss of specificity for these tasks. Furthermore, the taxonomic tables resulting from downstream processing provide biologically comparable results. However, we demonstrate that for taxonomic assignment, Bowtie2's specificity is still required. We suggest that periodic reevaluation of pipeline components, together with improvements to standardized

SUBMITTER: Armstrong G 

PROVIDER: S-EPMC9040843 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature