> 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-microbial-enrichment-plus/dragen-microbial-enrichment-plus/pipeline-logic.md). # 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 | --- # Agent Instructions This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com. ## Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://help.idm.illumina.com/dragen-microbial-enrichment-plus/dragen-microbial-enrichment-plus/pipeline-logic.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.