# Outputs Description

| Output File                                                 | Description                                                        |
| ----------------------------------------------------------- | ------------------------------------------------------------------ |
| **sample\_name-collapsed\_alignment\_summary\_metrics.txt** | Collapsed alignment metrics                                        |
| **sample\_name-duplex\_alignment\_summary\_metrics.txt**    | Collapsed Duplex alignment metrics                                 |
| **sample\_name-simplex\_alignment\_summary\_metrics.txt**   | Collapsed Simplex alignment metrics                                |
| **sample\_name-duplex\_family\_sizes.txt**                  | Duplex Family Size metrics                                         |
| **sample\_name-duplex\_umi\_counts.txt**                    | Duplex UMI count metrics                                           |
| **sample\_name-duplex\_yield\_metrics.txt**                 | Duplex yield metrics                                               |
| **sample\_name-family\_sizes.txt**                          | UMI Family Size metrics                                            |
| **sample\_name-umi\_counts.txt**                            | UMI Count metrics                                                  |
| **sample\_name-umi.hist.txt**                               | UMI histogram file                                                 |
| **sample\_name-group.bam**                                  | Grouped BAM for duplex metrics calculation outside of the workflow |
| **sample\_name-collapsed.bam**                              | Collapsed bam                                                      |
| **sample\_name-collapsed.bai**                              | Collapsed bam index                                                |
| **sample\_name-duplex.bam**                                 | Collapsed Duplex bam                                               |
| **sample\_name-duplex.bai**                                 | Collapsed Duplex bam index                                         |
| **sample\_name-simplex.bam**                                | Collapsed Simplex bam                                              |
| **csample\_name-simplex.bai**                               | Collapsed Simplex bam index                                        |
| **collapsed\_R1.fastq.gz**                                  | Collapsed Read 1 Fastq                                             |
| **collapsed\_R2.fastq.gz**                                  | Collapsed Read 2 Fastq                                             |
