Welcome to SEDNA Metagenomics
About
SEDNA Metagenomics is based on shotgun metagenomics sequencing of 612 samples from the Arctic Ocean. Reads were co-assembled into contigs using SPAdes, and locations were inferred based on differential abundance (read-mapping) estimates using BH t-SNE with the Rtsne package. Metagenome-assembled genome (MAG) bins were called using a taxonomy- and gene-aware single-linkage clustering algorithm. The globe is visualized with Cesium. Please direct questions and issues to the Github repo.
Tips
- Click the globe once to stop it from rotating. Click twice to resume.
- Hover over a contig to see information about the bin. Click to freeze the info box. Click empty space to unfreeze the box.
- Search by taxonomy or genes of interest using the search box. You may have to hit 'enter' after clicking on a suggested item.
Examples
- Bacteria
- Archaea
- Micromonas
- Viruses
- Alkane 1-monooxygenase
- Ammonia monooxygenase gamma subunit
- 16S ribosomal RNA (partial)
- Phage shock protein A
View community network data on SEDNA Community View
View ribosomal RNA data on SEDNA WorldTree View
More Information
Created by Eric Collins in the Cryomics Lab at the University of Alaska Fairbanks, with funding from the NOAA Office of Ocean Exploration and Research for the project Mapping the Uncharted Diversity of Arctic Marine Microbes.