> For the complete documentation index, see [llms.txt](https://help.idm.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.idm.illumina.com/dragen-16s-plus/dragen-16s-plus/pipeline-logic.md).

# Pipeline logic

## Pipeline steps

| Step                       | Description                                                                                                                                                                                                                                                                                                                                                                                                                                     | Notes                            |
| -------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------- |
| 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. For paired-end data, both read1 and read2 must pass QC filtering for the read pair to be used for analysis. It is assumed that appropriate adapter trimming has already been performed. | Optional                         |
| Taxonomic classification   | Read classification using the DRAGEN Kmer Classifier                                                                                                                                                                                                                                                                                                                                                                                            | Custom database can be specified |
| Result filters             | User-specified read count threshold \[0-1000] applied                                                                                                                                                                                                                                                                                                                                                                                           | Default is 0 or unfiltered       |
| Reporting - Analysis level | XLSX, CSV, HTML, ZIP                                                                                                                                                                                                                                                                                                                                                                                                                            |                                  |
| Reporting - Sample level   | JSON, CSV, HTML, TXT.GZ                                                                                                                                                                                                                                                                                                                                                                                                                         |                                  |


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