Browse the genome collection

  • Click on a genome to get to its database page, where you can see antismash results or download annotations.
  • Sort by multiple columns using pressing shift when clicking the sort icon.
  • To help you navigate the amount of columns you can toggle them based on categories...
  • Or reorder them to your liking (although due to the size of the dataset, that can be slow).
  • Global search is enabled with regex. 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.
  • More advanced: Using regex allows for multi-column search. Basically, the search function is applied to the table with a double space separator 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.*cluster_8` will filter MALA genomes annotated as p__Eremiobacterota by GTDB with Specl Species Cluster 8.
  • 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
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Select Id Genome GTDB Taxonomy Q score Completeness Contamination Tool N50 (scaffolds) # scaffolds GC Content Genome size CheckM Q score CheckM Completeness CheckM Contamination CheckM Strain heterogeneity CheckM version Anvio Q score Anvio Completion Anvio Redundancy Anvio Domain Anvio version Genome Path Biosample latitude longitude Publication
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