Meta2DB: Curated shotgun metagenomic feature sets and metadata for health state prediction.
Where this comes from
- Record sourced from PubMed, PMID 42384916.
- Also identified by DOI 10.1093/bioinformatics/btag422.
- No licence information is recorded for this record.
- Because redistribution is not established, this page shows the abstract only. Follow the links below for the full text.
Abstract
Meta2DB is a curated metagenomic and metadata database that provides structurally consistent microbiome taxonomy feature count tables for 13,897 samples across 84 studies, 23 disease states, and 34 geographical locations. All samples were uniformly processed using a streamlined metagenomic classification pipeline that employs a unique and comprehensive reference database indexed to contain all sequences across all kingdoms of life that were present in the NCBI Nucleotide (nt) database retrieved on January 04, 2023. This pipeline leverages high-performance computing (HPC) resources at Lawrence Livermore National Laboratory and was used to process 50TB of publicly available raw metagenomic sequence data. Extensive metadata curation was carried out through a combination of manual curation and automated parsing, producing a consistent inter-study metadata table specifically structured to facilitate training of ML models for prediction of human health. Data is available at https://gdo-meta2db.llnl.gov/ and https://zenodo.org/records/17315984. Supplementary data are available at Bioinformatics online.