NanoMGT: Marker gene typing of low complexity mono-species metagenomic samples using noisy long reads.

ABSTRACT: Rapid advancements in sequencing technologies have led to significant progress in microbial genomics, yet challenges persist in accurately identifying microbial strain diversity in metagenomic samples, especially when working with noisy long-read data from platforms like Oxford Nanopore Technologies (ONT). In this article, we introduce NanoMGT, a tool designed to enhance marker gene typing in low-complexity mono-species samples, leveraging the unique properties of long reads. NanoMGT excels in its ability to accurately identify mutations amidst high error rates, ensuring the reliable detection of multiple strain-specific marker genes. Our tool implements a novel scoring system that rewards mutations co-occurring across different reads and penalizes densely grouped, likely erroneous variant

SUBMITTER: Hallgren MB 

PROVIDER: S-EPMC11387619 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature