RAPiD: a rapid and accurate plant pathogen identification pipeline for on-site nanopore sequencing.

ABSTRACT: Nanopore sequencing technology has enabled the rapid, on-site taxonomic identification of samples from anything and anywhere. However, sequencing errors, inadequate databases, as well as the need for bioinformatic expertise and powerful computing resources, have hampered the widespread use of the technology for pathogen identification in the agricultural sector. Here we present RAPiD, a lightweight and accurate real-time taxonomic profiling pipeline. Compared to other metagenomic profilers, RAPiD had a higher classification precision achieved through the use of a curated, non-redundant database of common agricultural pathogens and extensive quality filtering of alignments. On a fungal, bacterial and mixed mock community RAPiD was the only pipeline to detect all members of the communities.

SUBMITTER: Knobloch S 

PROVIDER: S-EPMC11438431 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature