🚩Release notes
🚩 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
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
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
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