16s bioinformatics pipeline Search Results


16s pipeline bugseq (v5.0)  (BugSeq Bioinformatics)
90
BugSeq Bioinformatics 16s pipeline bugseq (v5.0)
Average relative abundance (%) of bacterial organisms present in MCM2α and MCM2β obtained by ONT sequencing using the R10.4.1 MinION flow cell and ONT <t>16S</t> Barcoding all-in-one kit (v14). Three concentrations of the MCM2α and MCM2β materials were tested in triplicate (neat, 1:10 and 1:100) and analysis by EPI2ME Desktop agent. The species abundance (%) of each dilution is reported, including the dPCR reported composition for the two materials ( <xref ref-type= Supplementary Data 3 ). " width="250" height="auto" />
16s Pipeline Bugseq (V5.0), supplied by BugSeq Bioinformatics, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/16s+bioinformatics+pipeline/bugseq+16s/pmc11922894-278-10-8
Average 90 stars, based on 1 article reviews
16s pipeline bugseq (v5.0) - by Bioz Stars, 2026-10
90/100 stars
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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
16s bioinformatic pipeline - by Bioz Stars, 2026-10
86/100 stars
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16s oxford nanopore long read protocol  (Oxford Nanopore)
90
Oxford Nanopore 16s oxford nanopore long read protocol
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 Oxford Nanopore Long Read Protocol, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/16s+bioinformatics+pipeline/16s+oxford+nanopore+long+read+protocol/pmc11112893-40-17-4
Average 90 stars, based on 1 article reviews
16s oxford nanopore long read protocol - by Bioz Stars, 2026-10
90/100 stars
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minion™ sequencer  (Oxford Nanopore)
90
Oxford Nanopore minion™ sequencer
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
Minion™ Sequencer, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/16s+bioinformatics+pipeline/minion+sequencer/pmc06396348-23-20-17
Average 90 stars, based on 1 article reviews
minion™ sequencer - by Bioz Stars, 2026-10
90/100 stars
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nanopore minion sequencer  (Oxford Nanopore)
90
Oxford Nanopore nanopore minion sequencer
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
Nanopore Minion Sequencer, supplied by Oxford Nanopore, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/16s+bioinformatics+pipeline/oxford+nanopore+sequencing/pm39869650-94-23-0
Average 90 stars, based on 1 article reviews
nanopore minion sequencer - by Bioz Stars, 2026-10
90/100 stars
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16s rrna v4 region  (Pyrosequencing Inc)
86
Pyrosequencing Inc 16s rrna v4 region
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 Rrna V4 Region, supplied by Pyrosequencing Inc, 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+pyrosequencing+rrna/pmc12429330-108-6-10
Average 86 stars, based on 1 article reviews
16s rrna v4 region - by Bioz Stars, 2026-10
86/100 stars
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miseq illumina sequencing platform  (Illumina Inc)
99
Illumina Inc miseq illumina sequencing platform
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
Miseq Illumina Sequencing Platform, supplied by Illumina Inc, 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/MiSeq+System/10__4172_slash_2161___0525__1000493-5-8-9
Average 99 stars, based on 1 article reviews
miseq illumina sequencing platform - by Bioz Stars, 2026-10
99/100 stars
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one codex pipeline  (Akoya Biosciences)
99
Akoya Biosciences one codex 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
One Codex Pipeline, supplied by Akoya Biosciences, 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/PhenoCycler-Fusion+2%2E0/pm30166151-541-50-51
Average 99 stars, based on 1 article reviews
one codex pipeline - by Bioz Stars, 2026-10
99/100 stars
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fastdna spin kit 193 for soil  (Valiant Co Ltd)
99
Valiant Co Ltd fastdna spin kit 193 for soil
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
Fastdna Spin Kit 193 For Soil, supplied by Valiant Co Ltd, 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/FastDNA+Spin+Kit/10__2139_slash_ssrn__4013649-90-24-30
Average 99 stars, based on 1 article reviews
fastdna spin kit 193 for soil - by Bioz Stars, 2026-10
99/100 stars
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saliva qiaamp dna blood mini kit  (Qiagen)
99
Qiagen saliva qiaamp dna blood mini kit
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
Saliva Qiaamp Dna Blood Mini Kit, supplied by Qiagen, 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/QIAamp+DNA+Blood+Mini+Kit/pmc12068744-39-37-50
Average 99 stars, based on 1 article reviews
saliva qiaamp dna blood mini kit - by Bioz Stars, 2026-10
99/100 stars
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clinqc  (SourceForge net)
90
SourceForge net clinqc
Popular Bioinformatics Tools Used for 16S rRNA Metagenome Analysis.
Clinqc, supplied by SourceForge net, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/16s+bioinformatics+pipeline/clinqc/pmc06363981-191-52-53
Average 90 stars, based on 1 article reviews
clinqc - by Bioz Stars, 2026-10
90/100 stars
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miseq reagent kit v3  (Illumina Inc)
99
Illumina Inc miseq reagent kit v3
Popular Bioinformatics Tools Used for 16S rRNA Metagenome Analysis.
Miseq Reagent Kit V3, supplied by Illumina Inc, 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/MiSeq+Reagent+Kit+v3/10__1002_slash_jper__18___0167-75-23-27
Average 99 stars, based on 1 article reviews
miseq reagent kit v3 - by Bioz Stars, 2026-10
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Image Search Results


Average relative abundance (%) of bacterial organisms present in MCM2α and MCM2β obtained by ONT sequencing using the R10.4.1 MinION flow cell and ONT 16S Barcoding all-in-one kit (v14). Three concentrations of the MCM2α and MCM2β materials were tested in triplicate (neat, 1:10 and 1:100) and analysis by EPI2ME Desktop agent. The species abundance (%) of each dilution is reported, including the dPCR reported composition for the two materials ( <xref ref-type= Supplementary Data 3 ). " width="100%" height="100%">

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: Standardization of 16S rRNA gene sequencing using nanopore long read sequencing technology for clinical diagnosis of culture negative infections

doi: 10.3389/fcimb.2025.1517208

Figure Lengend Snippet: Average relative abundance (%) of bacterial organisms present in MCM2α and MCM2β obtained by ONT sequencing using the R10.4.1 MinION flow cell and ONT 16S Barcoding all-in-one kit (v14). Three concentrations of the MCM2α and MCM2β materials were tested in triplicate (neat, 1:10 and 1:100) and analysis by EPI2ME Desktop agent. The species abundance (%) of each dilution is reported, including the dPCR reported composition for the two materials ( Supplementary Data 3 ).

Article Snippet: To ensure the quality of the output, the BugSeq (v5.0) 16S pipeline requires both 80% query coverage and 80% sequence identity for the classification of consensus sequences ( ).

Techniques: Sequencing

Average relative abundance (%) of bacterial organisms present in MCM2α and MCM2β obtained by ONT sequencing using the R10.4.1 MinION flow cell and the in-house developed 16S ONT RBK method. Three concentrations of the MCM2α and MCM2β materials were tested in triplicate (neat, 1:10 and 1:100) and amplified in two PCRs targeting the V1-V2 and V1-V9 genomic regions of the 16S rRNA gene; analysis by EPI2ME Desktop agent. The species abundance (%) of each dilution is reported, including the dPCR reported composition for the two materials ( <xref ref-type= Supplementary data 3 ). " width="100%" height="100%">

Journal: Frontiers in Cellular and Infection Microbiology

Article Title: Standardization of 16S rRNA gene sequencing using nanopore long read sequencing technology for clinical diagnosis of culture negative infections

doi: 10.3389/fcimb.2025.1517208

Figure Lengend Snippet: Average relative abundance (%) of bacterial organisms present in MCM2α and MCM2β obtained by ONT sequencing using the R10.4.1 MinION flow cell and the in-house developed 16S ONT RBK method. Three concentrations of the MCM2α and MCM2β materials were tested in triplicate (neat, 1:10 and 1:100) and amplified in two PCRs targeting the V1-V2 and V1-V9 genomic regions of the 16S rRNA gene; analysis by EPI2ME Desktop agent. The species abundance (%) of each dilution is reported, including the dPCR reported composition for the two materials ( Supplementary data 3 ).

Article Snippet: To ensure the quality of the output, the BugSeq (v5.0) 16S pipeline requires both 80% query coverage and 80% sequence identity for the classification of consensus sequences ( ).

Techniques: Sequencing, Amplification

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

Popular Bioinformatics Tools Used for 16S rRNA Metagenome Analysis.

Journal: Journal of Clinical and Experimental Hepatology

Article Title: Methods for Studying Gut Microbiota: A Primer for Physicians

doi: 10.1016/j.jceh.2018.04.016

Figure Lengend Snippet: Popular Bioinformatics Tools Used for 16S rRNA Metagenome Analysis.

Article Snippet: Details on the usage, selectable features, strengths and limitations of these tools are usually available on the servers where these are hosted. table ft1 table-wrap mode="anchored" t5 caption a7 Purpose Tools URL Trimming of primers and adapters Cutadapt https://github.com/marcelm/cutadapt Sickle https://github.com/najoshi/sickle cutPrimers https://github.com/aakechin/cutPrimers AdaperRemoval https://github.com/MikkelSchubert/adapterremoval Quality control NGS-QC ToolKit http://www.nipgr.res.in/ngsqctoolkit.html Trimmomatic http://www.usadellab.org/cms/?page=trimmomatic clinQC https://sourceforge.net/projects/clinqc/ AfterQC https://github.com/OpenGene/AfterQC Merger of paired-end reads Pandaseq https://github.com/neufeld/pandaseq PEAR https://sco.h-its.org/exelixis/web/software/pear/ FLASH https://ccb.jhu.edu/software/FLASH/ MeFiT https://github.com/nisheth/MeFiT 16S-rRNA metagenome analysis pipelines QIIME http://qiime.org/ MOTHUR https://www.mothur.org/ MG-RAST http://metagenomics.anl.gov/ MICCA http://micca.org/ Open in a separate window Popular Bioinformatics Tools Used for 16S rRNA Metagenome Analysis.

Techniques: Control