Prokaryotic fraction recovery using Tiara

If you are more interested in the prokaryotic fraction (for example during investigating bacterial endosymbionts of eukaryotes) we provide pipeline presented below:

The pipeline

1. Classify assembled contigs with tiara.
2. Take only sequences classified as prokarya (bacteria, archaea and prokarya classes).
3. Extract reads that map to prokaryotic fraction (you can skip this step).
4. Assemble again using Spades (you can skip this step).
5. Bin them using suitable software (metabat2/concoot).
6. Use tiara again for preliminary assessment of achieved bins (optional).
7. You can manually refine bins using Anvi’O. Further check quality of bins can be done using checkM. We strongly recommend to assign lineage to the bins using gtdb-tk.

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