About GLAMR


Updated on Nov. 8, 2024, 4 p.m.

The Great Lakes Atlas for Multi-omics Research (GLAMR) Database enables discovery and exploration of environmental ‘omics’ data from the Laurentian Great Lakes. The GLAMR database contains shotgun metagenomic and metatranscriptomic sequencing data, amplicon sequencing data, and associated metadata including collection and processing metadata, and nutrient and environmental measurements. GLAMR can currently be used to explore the content of metagenomic datasets; we are currently implementing similar exploration of metatranscriptomic and amplicon data sets.

GLAMR facilitates exploration of omics datasets, processed with standardized bioinformatics pipelines to enable comparison across studies. Where possible, GLAMR makes use of existing community standards to enable interoperability with other services.

GLAMR is a product of the Geomicrobiology Lab at the University of Michigan and is supported by the Cooperative Institute for Great Lakes Research through the NOAA ‘Omics program.

Abundance / contig annotation data for metagenomic samples are now based on an MMseqs2-based pipeline using the UniRef database with supplemental annotations from our Universal Multi-omics Reference and Alignment Database (UMRAD).

GLAMR software including bioinformatics pipelines and the website and database code are available via GitHub. The GLAMR bioinformatics pipelines are written using the Snakemake workflow engine, and the website is built using the Django framework backed by a Postgres database.

[previous GLAMR versions]

Credits

Reference data sources:

Bioinformatics tools:

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