Browse the genome collection

This page provides you with an interactive table to browse, search, filter the ~35,000 microbial genomes in the OMD. You can:

  • Click on a genome to get to its index page, where you can see antismash results or download annotations.
  • Sort a column by clicking on the arrows next to its names.
  • Sort by multiple columns by pressing shift when clicking on an additional column.
  • Select only a category of column to simplify the table.
  • Reorder the columns to your liking (although due to the size of the dataset, that can be slow).
  • Search for a word or pattern in the table using a global search with regex enabled. For instance, you can look for Tara genomes with `TARA_`, or use `_METAG_` to select MAGs only or `_REFG_` for reference genomes. MAGs from this study can be queried with `_METAG_[A-Z]{8}` (Excludes Tara MAGs from an other study). To make sure that you only pick up perfect matches, use `$` at the end of the word, e.g. `cluster_1$` will only pick up that cluster and not all numbers starting with 1.
  • Select rows by searching multiple column at once. With regex you can create the desired pattern using double space between columns, so, for instance `TARA_.*;p__Myxococcota;` will filter TARA genomes annotated as p__Myxococcota by GTDB ,`MARD_.*c*Actinobacteriota;` will filter MARD genomes annotated as p__Actinobacteriota by GTDB and `MALA_.*;p__Eremiobacterota.*C2$` will filter MALA genomes annotated as p__Eremiobacterota by GTDB belonging to the Species Cluster C2.
  • You can also move down to the search panes for per column and numeric filtering. Note that not all the columns are enabled (usually because they can either be searched or did not appear too useful), and they may not provide the best filtering options out of the box: feedback is welcome to improve the user experience.
  • Export a filtered table, or after applying visibility contraints as imposed by the Toggle Columns button or selected rows only with the export button. Prior to any export, selected rows should be ticked. To select all rows for export, click the Select All button first.
  • Depending on your computer/browser searching and filtering might take some time. For finer control and reactivity feel free to prefilter/select and export the table to work locally.
Genome Collection
Select Id Genome # Biosynthetic Regions # Biosynthetic Products RiPPs RiPPs:Proteusins NRPS PKSI Other PKS Saccharides Terpenes Other Mean Completeness Mean Contamination Differential Coverage Index CheckM Completeness CheckM Contamination CheckM Strain heterogeneity Anvio Completion Anvio Redundancy # tRNAs (AA) 16S rRNA 16S rRNA (partial) # CRISPRs GTDB Taxonomy Checkm Taxonomy Anvio Domain SpecI Species Cluster mOTUs Species Cluster dRep Species Cluster Dereplication Representative Genome Genome size # scaffolds N50 (scaffolds) Longest scaffold Coding density GC Content station depth depth layer latitude longitude date size fraction temperature (°C) oxygen (µmol/kg) detected in the water column