| Name | Type | Short Description |
|---|
| exclude-seqs | method | Exclude sequences by alignment |
| filter-reads | method | Filter demultiplexed sequences by alignment to reference database. |
| bowtie2-build | method | Build bowtie2 index from reference sequences. |
| decontam-identify | method | Identify contaminants |
| decontam-remove | method | Remove contaminants |
| evaluate-composition | visualizer | Evaluate expected vs. observed taxonomic composition of samples |
| evaluate-seqs | visualizer | Compare query (observed) vs. reference (expected) sequences. |
| evaluate-taxonomy | visualizer | Evaluate expected vs. observed taxonomic assignments |
| decontam-score-viz | visualizer | Generate a histogram representation of the scores |
| decontam-identify-batches | pipeline | Identify contaminants in Batch Mode |