4. Expected Output
| Output Type | Description |
|---|---|
| QC Reports | FastQC and MultiQC summary reports |
| Trimmed Reads | Quality-filtered sequencing reads (FASTQ) |
| Taxonomic Classification | Kraken2 classification reports & Krona plots |
| Genome Assembly | SPAdes-assembled contigs (FASTA) |
| AMR & Virulence Gene Detection | AMRFinderPlus, PlasmidFinder, and Gamma results |
| Phylogenetic & Similarity Analysis | FastANI and Mash distance matrices |
Last update: 2025-01-29