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README.md

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|[Stacked Barplot](https://github.com/PopovIILab/KrakenParser/wiki/Stacked-Barplot-API)|[Streamgraph](https://github.com/PopovIILab/KrakenParser/wiki/Streamgraph-API)|
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|![kpstbar](https://github.com/user-attachments/assets/916b0164-28be-4f49-9634-707408487b85)|![kpstream](https://github.com/user-attachments/assets/5c6d930c-e85f-4e2e-9dbf-8caefca49a76)|
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|![kpstbar](https://github.com/user-attachments/assets/916b0164-28be-4f49-9634-707408487b85)|![kpstream](https://github.com/user-attachments/assets/8fc09fdb-e397-4c39-9290-ad11da5335a8)|
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[Stacked Barplot + Streamgraph](https://github.com/PopovIILab/KrakenParser/wiki/Combined-Stacked-Barplot-&-Streamgraph)|[Clustermap](https://github.com/PopovIILab/KrakenParser/wiki/Clustermap)|
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|-------|-------|
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|![combined_white](https://github.com/user-attachments/assets/58acea93-f079-46fd-ac4b-d2ac83098c59)|![kpclust](https://github.com/user-attachments/assets/98a4d540-7c43-4802-8f77-277a5637a7a1)|
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|![combined_white](https://github.com/user-attachments/assets/48b3f6e3-6dd5-4298-a793-23dcd549e90c)|![kpclust](https://github.com/user-attachments/assets/98a4d540-7c43-4802-8f77-277a5637a7a1)|
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## Quick Start (Full Pipeline)
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To run the full pipeline, use the following command:
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│ │ ├─ counts_family.txt
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│ │ ├─ ...
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│ └─ csv/ # Total abundance CSV output
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├─ counts_species.csv
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├─ counts_genus.csv
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├─ counts_family.csv
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├─ ...
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├─ counts_species.csv
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├─ counts_genus.csv
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├─ counts_family.csv
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├─ ...
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├─ rel_abund/ # Relative abundance CSV output
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│ ├─ ra_species.csv
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│ ├─ ra_genus.csv

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