SituSeq: an offline protocol for rapid and remote Nanopore 16S rRNA amplicon sequence analysis.

ABSTRACT: Microbiome analysis through 16S rRNA gene sequencing is a crucial tool for understanding the microbial ecology of any habitat or ecosystem. However, workflows require large equipment, stable internet, and extensive computing power such that most of the work is performed far away from sample collection in both space and time. Performing amplicon sequencing and analysis at sample collection would have positive implications in many instances including remote fieldwork and point-of-care medical diagnoses. Here we present SituSeq, an offline and portable workflow for the sequencing and analysis of 16S rRNA gene amplicons using Nanopore sequencing and a standard laptop computer. SituSeq was validated by comparing Nanopore 16S rRNA gene amplicons, Illumina 16S rRNA gene amplicons, and Illumina me

SUBMITTER: Zorz J 

PROVIDER: S-EPMC10119094 | biostudies-literature | 2023 Apr

REPOSITORIES: biostudies-literature