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16s bioinformatics pipeline  (Zymo Research)


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    Zymo Research 16s bioinformatics pipeline
    16s Bioinformatics Pipeline, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 1160 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/16s+bioinformatics+pipeline/16S/us12473601-345-117-115
    Average 99 stars, based on 1160 article reviews
    16s bioinformatics pipeline - by Bioz Stars, 2026-10
    99/100 stars

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    Article Title: Methods for species-level resolution of microorganisms
    Article Snippet: Zymo Qiime + Phylum Species Research GreenGenes Euryarchaeota Methanobrevibacter ✓ x smithii Actinobacteria Bifidobacterium ✓ ✓ adolescentis Actinobacteria Bifidobacterium ✓ x angulatum Actinobacteria Bifidobacterium ✓ x ruminantium Actinobacteria Collinsella aerofaciens ✓ ✓ Bacteroidetes Bacteroides fragilis ✓ ✓ Bacteroidetes Prevotella copri ✓ ✓ Bacteroidetes Sphingobacteriaceae sp. ✓ x Firmicutes Catenibacterium mitsuokai ✓ x Firmicutes Clostridium difficile ✓ x Firmicutes Dialister invisus ✓ x Firmicutes Eubacterium rectale ✓ x Firmicutes Lactobacillus fermentum ✓ x Fusobacteria Fusobacterium nucleatum ✓ x Lentisphaerae Victivallis vadensis ✓ x Proteobacteria Bilophila wadsworthia ✓ x Proteobacteria Escherichia coli ✓ x Proteobacteria Sutterella wadsworthensis ✓ x Synergistetes Pyramidobacter piscolens ✓ ✓ Verrucomicrobia Akkermansia muciniphila ✓ ✓ Profiling previously unknown species in fecal samples: The Zymo Research 16S bioinformatics pipeline together with the present 16S database enabled species-level resolution even to previously unknown species.

    Article Title: Methods for species-level resolution of microorganisms
    Article Snippet: TABLE 1 Analysis of a mock microbial community mimicking human gut with Zymo Research’s 16S pipeline as compared to the Qiime Pipeline Phylum Species Zymo Research Qiime + GreenGenes Euryarchaeoto Methanobrevibacter smithii √ × Actinobacteria Bifidobacterium adolescentis √ √ Actinobacteria Bifidobacterium angulatum √ × Actinobacteria Bifidobacterium ruminantium √ × Actinobacteria Collinsella aerofaciens √ √ Bacteroidetes Bacteroides fragilis √ √ Bacteroidetes Prevotella copri √ √ Bacteroidetes Sphingobacteriaceae sp. √ × Firmicutes Catenibacterium mitsuokai √ × Firmicutes Clostridium difficile √ × Firmicutes Dialister invisus √ × Firmicutes Eubacterium rectale √ × Firmicutes Lactobacillus fermentum √ × Fusobacteria Fusobacterium nucleatum √ × Lentisphaerae Victivallis vadensis √ × Proteobacteria Bilophila wadsworthia √ × Proteobacteria Escherichia coli √ × Proteobacteria Sutterella wadsworthensis √ × Synergistetes Pyramidobacter piscolens √ √ Verrucomicrobia Akkermansia muciniphila √ √ Profiling previously unknown species in fecal samples: The Zymo Research 16S bioinformatics pipeline together with the present 16S database enabled species-level resolution even to previously unknown species.



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    16s bioinformatics pipeline  (Zymo Research)
    99
    Zymo Research 16s bioinformatics pipeline
    16s Bioinformatics Pipeline, supplied by Zymo Research, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/16s+bioinformatics+pipeline/16S/us12473601-345-117-115
    Average 99 stars, based on 1 article reviews
    16s bioinformatics pipeline - by Bioz Stars, 2026-10
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    16s bioinformatic pipeline  (1928 Diagnostics)
    86
    1928 Diagnostics 16s bioinformatic pipeline
    Workflow overview used by the participating laboratories. Seven different extraction methods were followed by library preparation using a modified ONT <t>16S</t> Barcoding kit 24 V14 protocol (52 °C annealing, 40 cycles), or in-house PCR systems with the Ligation Sequencing V14 kit. Sequencing was conducted on various ONT devices. Species identification was performed using the commercial 1928 Diagnostics-16S pipeline and the GMS-16S pipeline (EMU classification tool). Created in BioRender. Wang, H. (2024) https://BioRender.com/i45i214
    16s Bioinformatic Pipeline, supplied by 1928 Diagnostics, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/16s+bioinformatics+pipeline/16s+pipeline/pmc12321653-4-2-6
    Average 86 stars, based on 1 article reviews
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    Workflow overview used by the participating laboratories. Seven different extraction methods were followed by library preparation using a modified ONT 16S Barcoding kit 24 V14 protocol (52 °C annealing, 40 cycles), or in-house PCR systems with the Ligation Sequencing V14 kit. Sequencing was conducted on various ONT devices. Species identification was performed using the commercial 1928 Diagnostics-16S pipeline and the GMS-16S pipeline (EMU classification tool). Created in BioRender. Wang, H. (2024) https://BioRender.com/i45i214

    Journal: European Journal of Clinical Microbiology & Infectious Diseases

    Article Title: Nationwide multicentre study of Nanopore long-read sequencing for 16S rRNA-species identification

    doi: 10.1007/s10096-025-05158-w

    Figure Lengend Snippet: Workflow overview used by the participating laboratories. Seven different extraction methods were followed by library preparation using a modified ONT 16S Barcoding kit 24 V14 protocol (52 °C annealing, 40 cycles), or in-house PCR systems with the Ligation Sequencing V14 kit. Sequencing was conducted on various ONT devices. Species identification was performed using the commercial 1928 Diagnostics-16S pipeline and the GMS-16S pipeline (EMU classification tool). Created in BioRender. Wang, H. (2024) https://BioRender.com/i45i214

    Article Snippet: The commercial 16S bioinformatic pipeline from 1928 Diagnostics (1928-16S) was evaluated and compared with the open-sourced gms_16S pipeline that is based on the EMU classification tool (GMS-16S).

    Techniques: Extraction, Modification, Ligation, Sequencing

    Relative abundance (%) of reads per sample for each laboratory ( r-y ) and species using the GMS-16S pipeline. (a) monomicrobial QCMD samples (top), (b) monomicrobial GMS samples (middle) (c) polymicrobial samples for both sample sets (bottom). Bacterial load (CFU/mL) is provided for the GMS panel, while QCMD concentrations are unknown (N/A). See Supplementary file for detailed classification

    Journal: European Journal of Clinical Microbiology & Infectious Diseases

    Article Title: Nationwide multicentre study of Nanopore long-read sequencing for 16S rRNA-species identification

    doi: 10.1007/s10096-025-05158-w

    Figure Lengend Snippet: Relative abundance (%) of reads per sample for each laboratory ( r-y ) and species using the GMS-16S pipeline. (a) monomicrobial QCMD samples (top), (b) monomicrobial GMS samples (middle) (c) polymicrobial samples for both sample sets (bottom). Bacterial load (CFU/mL) is provided for the GMS panel, while QCMD concentrations are unknown (N/A). See Supplementary file for detailed classification

    Article Snippet: The commercial 16S bioinformatic pipeline from 1928 Diagnostics (1928-16S) was evaluated and compared with the open-sourced gms_16S pipeline that is based on the EMU classification tool (GMS-16S).

    Techniques:

    a Comparison of species identification between GMS-16S and 1928-16S for samples with the largest discrepancies (G12-G4). The relative abundance (%) for each laboratory is represented by a box, with similar identification on the left and differences on the right . See Supplementary File and for details. b Comparison of species distribution in the polymicrobial samples G11 and Q6 across the laboratories ( a - y ). Relative abundance (%) of reads are shown for both pipelines (GMS-16S vs 1928-16S)

    Journal: European Journal of Clinical Microbiology & Infectious Diseases

    Article Title: Nationwide multicentre study of Nanopore long-read sequencing for 16S rRNA-species identification

    doi: 10.1007/s10096-025-05158-w

    Figure Lengend Snippet: a Comparison of species identification between GMS-16S and 1928-16S for samples with the largest discrepancies (G12-G4). The relative abundance (%) for each laboratory is represented by a box, with similar identification on the left and differences on the right . See Supplementary File and for details. b Comparison of species distribution in the polymicrobial samples G11 and Q6 across the laboratories ( a - y ). Relative abundance (%) of reads are shown for both pipelines (GMS-16S vs 1928-16S)

    Article Snippet: The commercial 16S bioinformatic pipeline from 1928 Diagnostics (1928-16S) was evaluated and compared with the open-sourced gms_16S pipeline that is based on the EMU classification tool (GMS-16S).

    Techniques: Comparison