# Pipeline logic

#### Pipeline steps

| Step                               | Description                                                                                                                                                                                                                                                                                                                         | Notes                                                        | RPIP | UPIP | RVOP/RVEK | VSP | VSP V2 | Custom Panel |
| ---------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------ | :--: | :--: | :-------: | :-: | :----: | :----------: |
| Read QC                            | Low-quality bases are trimmed from the ends of each read. After trimming, the read is discarded if fewer than 50% of its bases have a quality score greater or equal to q20, the read is shorter than 32 bp, or the read has 5 or more ambiguous bases. It is assumed that appropriate adapter trimming has already been performed. | Optional                                                     |   X  |   X  |     X     |  X  |    X   |       X      |
| Dehosting                          | Human read removal using the DRAGEN Kmer Classifier                                                                                                                                                                                                                                                                                 |                                                              |   X  |   X  |     X     |  X  |    X   |       X      |
| Sample QC                          | Sample composition and enrichment factor calculations                                                                                                                                                                                                                                                                               | Internal control required to calculate the enrichment factor |   X  |   X  |           |     |    X   |              |
| Microorganism classification       | Pre-alignment filtering step                                                                                                                                                                                                                                                                                                        | Configurable sensitivity                                     |      |      |     X     |  X  |    X   |              |
| Microorganism detection            | Reference alignment, consensus sequence generation, variant calling                                                                                                                                                                                                                                                                 |                                                              |   X  |   X  |     X     |  X  |    X   |       X      |
| Microorganism quantification       | Absolute copies/mL calculation                                                                                                                                                                                                                                                                                                      | Quantitative internal control and concentration required     |   X  |   X  |           |     |    X   |              |
| Microorganism reporting thresholds | Proprietary algorithms or user-defined reporting logic                                                                                                                                                                                                                                                                              |                                                              |   X  |   X  |     X     |  X  |    X   |              |
| Bacterial AMR marker analysis      | Nucleotide and protein alignment, consensus sequence generation, variant calling and annotation                                                                                                                                                                                                                                     |                                                              |   X  |   X  |           |     |        |              |
| Viral AMR marker analysis          | Variant calling and annotation                                                                                                                                                                                                                                                                                                      |                                                              |   X  |      |     X     |  X  |    X   |              |
| Viral clade and lineage prediction | Pangolin, Nextclade                                                                                                                                                                                                                                                                                                                 |                                                              |   X  |      |     X     |  X  |    X   |              |
| Result filters                     | User-specified filters applied                                                                                                                                                                                                                                                                                                      |                                                              |   X  |   X  |     X     |  X  |    X   |              |
| Reporting - Analysis level         | XLSX, HTML, ZIP                                                                                                                                                                                                                                                                                                                     |                                                              |   X  |   X  |     X     |  X  |    X   |       X      |
| Reporting - Sample level           | JSON, HTML, FASTA (consensus sequences), VCF (viral variants)                                                                                                                                                                                                                                                                       |                                                              |   X  |   X  |     X     |  X  |    X   |       X      |