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Corrects typo
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mbdabrowska1 committed Mar 11, 2024
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- Filter out samples with no reads left after FASTP.
- Run ([`FASTQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) on the processed reads.

4. **Classfy and Cluster:**
4. **Classify and Cluster:**
- If specified, remove unclassified reads using ([`KRAKEN2`](https://github.com/DerrickWood/kraken2)).
- Subset reads based on specified parameters (default 100k reads to keep memory requirements reasonable).
- Perform k-mer frequency analysis with KMER_FREQS.
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9. **Generate Reports:**
- If report generation is chosen:
- Generate HTML reports.

## Usage

> **Note**
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