> 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/release-notes.md). # Release notes #### DRAGEN Microbial Enrichment Plus app version 1.1.0 **Component versions** * Test type, version: * RPIP 6.5.1 * UPIP 8.6.0 * RVOP 2.7.0 * VSP 2.7.0 * VSPv2 2.7.0 * Custom 1.0.0 * Analysis Pipeline version: 6.3.12 * DRAGEN version: 4.3.11 **Third-party versions** * Pangolin 4.3.1 (Pangolin database PUSHER version 1.27) * Nextclade 3.5.0 * SnpEff 5.1 * ResFinder (version 2.2.1) * NCBI Reference Gene Catalog (version 2023-09-26.1) * EUCAST expert rules on indicator agents (2019-2023) * CLSI Performance Standards for Antimicrobial Susceptibility Testing (M100 34th Edition) * Comprehensive Antibiotic Research Database (CARD, version 3.2.8) * Comprehensive Antibiotic Research Database Prevalence Data (CARD Prevalence, version 4.0.1) * World Health Organization (WHO) Influenza virus neuraminidase inhibitor (NAI) and polymerase acidic protein inhibitor (PAI) Reduced Susceptibility Marker Tables (07 March 2023 version) **Key updates** * Various bug fixes (see below) * Tiered reporting added for Norovirus (GI, GII, GIV, GVIII, GIX) and Dengue virus (type 1, type 2, type 3, type 4) * Tiered reporting suppressed for below subtype resolution of Influenza A virus subtypes H1N1 and H3N2 * Nextclade datasets added for Measles virus (MV) and Dengue virus (DENV) clade assignment * Reference genomes added for Monkeypox virus (MPV) Clade 1b * Additional database curation **Known issues** * When reading Biosamples from a Project, Fastq files for Biosamples sharing the same sample name prefix before the first underscore are merged. For example, Fastq files for Biosamples PREFIX\_001 and PREFIX\_002 will be merged and reported as a single PREFIX sample. To avoid this error, ensure that sample names are unique before the first underscore, replace underscores with a hyphen, or provide Biosample input from a list * Coverage results for SARS-CoV-2 are slightly (<1%) over-estimated, which may result in coverage >100% due to an error accounting for masked polyA-tail bases * Viral genome consensus sequence bases without aligned read support are indicated by "X" bases rather than "N" bases for RPIP viruses except SARS-CoV-2 and Influenza viruses * Variant annotation information for Influenza A and B viruses, including antiviral resistance prediction results, may not be populated when below threshold reporting is enabled and/or a user-defined microorganism reporting file is specified that does not include all members of the Influenza A and B virus tiered reporting groups. If viral variant annotation is of interest for Influenza A and B viruses, default microorganism reporting options are recommended **Known limitations** * When providing Biosample input from a list, 99 associated Fastq files is the maximum allowed per analysis. There is no Fastq file limitation when reading Biosamples from a Project * In strains containing insertion-deletion mutations (indels), there is a risk of false positive or false negative results for other resistance mutations within a region of 100 nucleotides around the indel * In strains containing long insertion-deletion mutations (indels), there is a risk of false negative results for two large vAMR-associated deletion mutations (RPIP, VSPv2) and one large bAMR-associated insertion mutation (RPIP). Long indels may be incorrectly reported as other variant types, such as frameshift mutations * Small differences in SARS-CoV-2 and Influenza virus results may be observed between repeat analyses **Bug fixes** * Nextclade parsing errors for some samples * Custom reference sequence analysis not functional in non-US regions * User-defined microorganism reporting feature not reporting microorganisms that belong to a tiered reporting group when “prediction\_logic” column set to “default” * RPKM and absolute quantity metrics inaccurate when read QC disabled * SHV beta-lactamase AMR markers incorrectly reported as carbapenemases based on a known curation error in CARD version 3.2.8 * Reads duplicated for samples with a single FASTQ file * Empty FASTQ files abort analysis * Pangolin not run on all samples with SARS-CoV-2 detected * Viral genome coverage plots not rendered for segmented viruses when all segments not detected * Description information missing for some viral genome accessions #### DRAGEN Microbial Enrichment Plus app version 1.0.0 Initial release. **Component versions** * Test type, version: * RPIP 6.3.0 * UPIP 8.4.0 * RVOP 2.3.0 * VSP 2.3.0 * VSPv2 2.3.0 * Custom 1.0.0 * Analysis Pipeline version: 6.3.12 * DRAGEN version: 4.3.6 **Third-party versions** * Pangolin 4.3.1 (Pangolin data 1.27) * Nextclade 3.5.0 * SnpEff 5.1 * ResFinder (version 2.2.1) * NCBI Reference Gene Catalog (version 2023-09-26.1) * EUCAST expert rules on indicator agents (2019-2023) * CLSI Performance Standards for Antimicrobial Susceptibility Testing (M100 34th Edition) * Comprehensive Antibiotic Research Database (CARD, version 3.2.8) * Comprehensive Antibiotic Research Database Prevalence Data (CARD Prevalence, version 4.0.1) * World Health Organization (WHO) Influenza virus neuraminidase inhibitor (NAI) and polymerase acidic protein inhibitor (PAI) Reduced Susceptibility Marker Tables (07 March 2023 version) **Key updates** * Updated and expanded microorganism and bacterial AMR marker databases * Updated and expanded Influenza virus typing capability and antiviral resistance (AVR) reporting * User-defined microorganism reporting list and reporting thresholds * Below threshold reporting for microorganisms and/or AMR markers * Custom reference sequence analysis **Known issues** * When reading Biosamples from a Project, Fastq files for Biosamples sharing the same sample name prefix before the first underscore are merged. For example, Fastq files for Biosamples PREFIX\_001 and PREFIX\_002 will be merged and reported as a single PREFIX sample. To avoid this error, ensure that sample names are unique before the first underscore, replace underscores with a hyphen, or provide Biosample input from a list * Reads are duplicated for samples with a single FASTQ file * Empty FASTQ files will abort analysis * Nextclade may encounter a parsing error for some samples. If an analysis fails, try re-running the analysis with Nextclade disabled * Pangolin may not be run on all samples with SARS-COV-2 detected * Custom reference sequence analysis is not functional in non-US regions * The user-defined microorganism reporting feature does not report microorganisms that belong to a tiered reporting group when the “prediction\_logic” column is set to “default”. See the User Guide for further information about microorganism tiered reporting * RPKM and absolute quantity metrics are inaccurate when read QC is disabled * SHV beta-lactamase AMR markers are incorrectly reported as carbapenemases based on a known curation error in CARD version 3.2.8 * Coverage results for SARS-CoV-2 are slightly (<1%) over-estimated, which may result in coverage >100% due to an error accounting for masked polyA-tail bases * Viral genome consensus sequence bases without aligned read support are indicated by "X" bases rather than "N" bases for RPIP viruses except SARS-CoV-2 and Influenza viruses * Variant annotation information for Influenza A and B viruses, including antiviral resistance prediction results, may not be populated when below threshold reporting is enabled and/or a user-defined microorganism reporting file is specified that does not include all members of the Influenza A and B virus tiered reporting groups. If viral variant annotation is of interest for Influenza A and B viruses, default microorganism reporting options are recommended **Known limitations** * When providing Biosample input from a list, 99 associated Fastq files is the maximum allowed per analysis. There is no Fastq file limitation when reading Biosamples from a Project * Small differences in results may be observed between repeat analyses * In strains containing insertion-deletion mutations (indels), there is a risk of false positive or false negative results for other resistance mutations within a region of 100 nucleotides around the indel * In strains containing long insertion-deletion mutations (indels), there is a risk of false negative results for two large vAMR-associated deletion mutations (RPIP, VSPv2) and one large bAMR-associated insertion mutation (RPIP). Long indels may be incorrectly reported as other variant types, such as frameshift mutations * The RPIP, VSPv2, VSPv1, and RVOP Data Analysis solutions can report Influenza A virus subtypes H1N1 and H3N2 to a below-subtype resolution. Multiple results for H1N1 and/or H3N2 may be reported concurrently, particularly in samples that contain a mixture of Influenza A virus subtypes * Viral genome coverage plots are not rendered for segmented viruses when all segments are not detected * Description information is missing for some viral genome accessions --- # 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. 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