Dataset Information

CgMSI: pathogen detection within species from nanopore metagenomic sequencing data.

ABSTRACT:

Background

Metagenomic sequencing is an unbiased approach that can potentially detect all the known and unidentified strains in pathogen detection. Recently, nanopore sequencing has been emerging as a highly potential tool for rapid pathogen detection due to its fast turnaround time. However, identifying pathogen within species is nontrivial for nanopore sequencing data due to the high sequencing error rate.

Results

We developed the core gene alleles metagenome strain identification (cgMSI) tool, which uses a two-stage maximum a posteriori probability estimation method to detect pathogens at strain level from nanopore metagenomic sequencing data at low computational cost. The cgMSI tool can accurately identify strains and estimate relative abundance at 1× coverage.

Conclusions

We developed cgMSI for nanopore metagenomic pathogen detection within species. cgMSI is available at https://github.com/ZHU-XU-xmu/cgMSI .

SUBMITTER: Zhu X

PROVIDER: S-EPMC10568937 | biostudies-literature | 2023 Oct

REPOSITORIES: biostudies-literature

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Publications

cgMSI: pathogen detection within species from nanopore metagenomic sequencing data.

Zhu Xu X Zhao Lili L Huang Lihong L Yang Wenxian W Wang Liansheng L Yu Rongshan R

BMC bioinformatics 20231012 1

<h4>Background</h4>Metagenomic sequencing is an unbiased approach that can potentially detect all the known and unidentified strains in pathogen detection. Recently, nanopore sequencing has been emerging as a highly potential tool for rapid pathogen detection due to its fast turnaround time. However, identifying pathogen within species is nontrivial for nanopore sequencing data due to the high sequencing error rate.<h4>Results</h4>We developed the core gene alleles metagenome strain identificati ...[more]

PMID: 37821827

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