🚩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

• 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