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Overall study design and bioinformatic analysis workflow. Overview of the experimental and analytical framework used in this study. Paired stool samples from children and their caregivers underwent DNA extraction, while the Zymo mock community, provided as ready-to-use DNA, served as a reference standard. All samples were prepared for <t>sequencing</t> using an Ion <t>16S</t> metagenomics kit. Resulting FASTQ files were processed through a comparative pipeline assessment step, in which multiple V-region pipelines (V2–9) were evaluated to ensure robust performance. Following validation, the selected workflows were applied to the full data set, culminating in final analyses that encompassed microbial variant profiling, differential abundance testing, and ratio-based microbiome assessments.
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Overall study design and bioinformatic analysis workflow. Overview of the experimental and analytical framework used in this study. Paired stool samples from children and their caregivers underwent DNA extraction, while the Zymo mock community, provided as ready-to-use DNA, served as a reference standard. All samples were prepared for <t>sequencing</t> using an Ion <t>16S</t> metagenomics kit. Resulting FASTQ files were processed through a comparative pipeline assessment step, in which multiple V-region pipelines (V2–9) were evaluated to ensure robust performance. Following validation, the selected workflows were applied to the full data set, culminating in final analyses that encompassed microbial variant profiling, differential abundance testing, and ratio-based microbiome assessments.
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Overall study design and bioinformatic analysis workflow. Overview of the experimental and analytical framework used in this study. Paired stool samples from children and their caregivers underwent DNA extraction, while the Zymo mock community, provided as ready-to-use DNA, served as a reference standard. All samples were prepared for <t>sequencing</t> using an Ion <t>16S</t> metagenomics kit. Resulting FASTQ files were processed through a comparative pipeline assessment step, in which multiple V-region pipelines (V2–9) were evaluated to ensure robust performance. Following validation, the selected workflows were applied to the full data set, culminating in final analyses that encompassed microbial variant profiling, differential abundance testing, and ratio-based microbiome assessments.
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Overall study design and bioinformatic analysis workflow. Overview of the experimental and analytical framework used in this study. Paired stool samples from children and their caregivers underwent DNA extraction, while the Zymo mock community, provided as ready-to-use DNA, served as a reference standard. All samples were prepared for <t>sequencing</t> using an Ion <t>16S</t> metagenomics kit. Resulting FASTQ files were processed through a comparative pipeline assessment step, in which multiple V-region pipelines (V2–9) were evaluated to ensure robust performance. Following validation, the selected workflows were applied to the full data set, culminating in final analyses that encompassed microbial variant profiling, differential abundance testing, and ratio-based microbiome assessments.
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Overall study design and bioinformatic analysis workflow. Overview of the experimental and analytical framework used in this study. Paired stool samples from children and their caregivers underwent DNA extraction, while the Zymo mock community, provided as ready-to-use DNA, served as a reference standard. All samples were prepared for <t>sequencing</t> using an Ion <t>16S</t> metagenomics kit. Resulting FASTQ files were processed through a comparative pipeline assessment step, in which multiple V-region pipelines (V2–9) were evaluated to ensure robust performance. Following validation, the selected workflows were applied to the full data set, culminating in final analyses that encompassed microbial variant profiling, differential abundance testing, and ratio-based microbiome assessments.
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Overall study design and bioinformatic analysis workflow. Overview of the experimental and analytical framework used in this study. Paired stool samples from children and their caregivers underwent DNA extraction, while the Zymo mock community, provided as ready-to-use DNA, served as a reference standard. All samples were prepared for <t>sequencing</t> using an Ion <t>16S</t> metagenomics kit. Resulting FASTQ files were processed through a comparative pipeline assessment step, in which multiple V-region pipelines (V2–9) were evaluated to ensure robust performance. Following validation, the selected workflows were applied to the full data set, culminating in final analyses that encompassed microbial variant profiling, differential abundance testing, and ratio-based microbiome assessments.
Rhapsody Sequence Analysis Pipeline, supplied by Becton Dickinson, 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/result/rhapsody sequence analysis pipeline/product/Becton Dickinson
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rhapsody sequence analysis pipeline - by Bioz Stars, 2026-05
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sanger sequencing and ice analysis pipeline  (Synthego Inc)
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Overall study design and bioinformatic analysis workflow. Overview of the experimental and analytical framework used in this study. Paired stool samples from children and their caregivers underwent DNA extraction, while the Zymo mock community, provided as ready-to-use DNA, served as a reference standard. All samples were prepared for <t>sequencing</t> using an Ion <t>16S</t> metagenomics kit. Resulting FASTQ files were processed through a comparative pipeline assessment step, in which multiple V-region pipelines (V2–9) were evaluated to ensure robust performance. Following validation, the selected workflows were applied to the full data set, culminating in final analyses that encompassed microbial variant profiling, differential abundance testing, and ratio-based microbiome assessments.
Sanger Sequencing And Ice Analysis Pipeline, supplied by Synthego Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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sanger sequencing and ice analysis pipeline - by Bioz Stars, 2026-05
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amplicon sequencing analysis pipeline (asap)  (Illumina Inc)
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Overall study design and bioinformatic analysis workflow. Overview of the experimental and analytical framework used in this study. Paired stool samples from children and their caregivers underwent DNA extraction, while the Zymo mock community, provided as ready-to-use DNA, served as a reference standard. All samples were prepared for <t>sequencing</t> using an Ion <t>16S</t> metagenomics kit. Resulting FASTQ files were processed through a comparative pipeline assessment step, in which multiple V-region pipelines (V2–9) were evaluated to ensure robust performance. Following validation, the selected workflows were applied to the full data set, culminating in final analyses that encompassed microbial variant profiling, differential abundance testing, and ratio-based microbiome assessments.
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amplicon sequencing analysis pipeline (asap) - by Bioz Stars, 2026-05
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rna-seq qc and sequencing pipeline and read analysis  (Beijing Genomics Institute Shenzhen)
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Overall study design and bioinformatic analysis workflow. Overview of the experimental and analytical framework used in this study. Paired stool samples from children and their caregivers underwent DNA extraction, while the Zymo mock community, provided as ready-to-use DNA, served as a reference standard. All samples were prepared for <t>sequencing</t> using an Ion <t>16S</t> metagenomics kit. Resulting FASTQ files were processed through a comparative pipeline assessment step, in which multiple V-region pipelines (V2–9) were evaluated to ensure robust performance. Following validation, the selected workflows were applied to the full data set, culminating in final analyses that encompassed microbial variant profiling, differential abundance testing, and ratio-based microbiome assessments.
Rna Seq Qc And Sequencing Pipeline And Read Analysis, supplied by Beijing Genomics Institute Shenzhen, 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/result/rna-seq qc and sequencing pipeline and read analysis/product/Beijing Genomics Institute Shenzhen
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rna-seq qc and sequencing pipeline and read analysis - by Bioz Stars, 2026-05
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Overall study design and bioinformatic analysis workflow. Overview of the experimental and analytical framework used in this study. Paired stool samples from children and their caregivers underwent DNA extraction, while the Zymo mock community, provided as ready-to-use DNA, served as a reference standard. All samples were prepared for sequencing using an Ion 16S metagenomics kit. Resulting FASTQ files were processed through a comparative pipeline assessment step, in which multiple V-region pipelines (V2–9) were evaluated to ensure robust performance. Following validation, the selected workflows were applied to the full data set, culminating in final analyses that encompassed microbial variant profiling, differential abundance testing, and ratio-based microbiome assessments.

Journal: Microbiology Spectrum

Article Title: QIIME2 enhances multi-amplicon sequencing data analysis: a standardized and validated open-source pipeline for comprehensive 16S rRNA gene profiling

doi: 10.1128/spectrum.01673-25

Figure Lengend Snippet: Overall study design and bioinformatic analysis workflow. Overview of the experimental and analytical framework used in this study. Paired stool samples from children and their caregivers underwent DNA extraction, while the Zymo mock community, provided as ready-to-use DNA, served as a reference standard. All samples were prepared for sequencing using an Ion 16S metagenomics kit. Resulting FASTQ files were processed through a comparative pipeline assessment step, in which multiple V-region pipelines (V2–9) were evaluated to ensure robust performance. Following validation, the selected workflows were applied to the full data set, culminating in final analyses that encompassed microbial variant profiling, differential abundance testing, and ratio-based microbiome assessments.

Article Snippet: To establish a standardized 16S rRNA sequencing analysis pipeline, five replicates of mock microbial DNA standards were analyzed using QIIME2, benchmarked against IR and the theoretical Zymo mock composition ( ).

Techniques: DNA Extraction, Sequencing, Biomarker Discovery, Variant Assay

Influence of caregiver microbiota on pediatric patient gut microbiome composition. ( A ) PCoA based on UniFrac distances, illustrating the gut microbial community structure of pediatric patients (triangles) and their caregivers (circles). Each child-caregiver pair is connected by a gray line. Pediatric samples were designated as high‐ (violet) or low‐similarity (green) depending on whether their correlation with the caregiver was significant ( P value ≤ 0.05) and their Euclidean distance in the PCoA space fell below 0.255. ( B ) Bubble plot showing the correlation strength (Pearson’s correlation) between child and caregiver microbiomes for each family. Bubble size indicates the –log( P value), reflecting statistical significance, while bubble color corresponds to whether each family falls into the high‐ (violet) or low‐similarity (green) group. ( C ) Box plots depicting two alpha diversity metrics (Faith’s phylogenetic diversity and observed features, i.e., ASV richness) for pediatric samples in the high‐ and low‐similarity groups. ( D ) Differential abundance analysis using DESeq2, comparing high‐ (violet) versus low‐similarity (green) groups. Significantly differentially abundant ASVs (|Log2FoldChange| > 1, FDR < 0.05) are listed by taxonomic affiliation alongside the number of ASVs per taxon. Blue‐highlighted species names indicate >99% sequence identity to entries in the NCBI 16S rRNA database, confirming species‐level identification. In the bubble plot, circle size represents –log10(FDR), and color indicates the similarity group in which the ASV is enriched.

Journal: Microbiology Spectrum

Article Title: QIIME2 enhances multi-amplicon sequencing data analysis: a standardized and validated open-source pipeline for comprehensive 16S rRNA gene profiling

doi: 10.1128/spectrum.01673-25

Figure Lengend Snippet: Influence of caregiver microbiota on pediatric patient gut microbiome composition. ( A ) PCoA based on UniFrac distances, illustrating the gut microbial community structure of pediatric patients (triangles) and their caregivers (circles). Each child-caregiver pair is connected by a gray line. Pediatric samples were designated as high‐ (violet) or low‐similarity (green) depending on whether their correlation with the caregiver was significant ( P value ≤ 0.05) and their Euclidean distance in the PCoA space fell below 0.255. ( B ) Bubble plot showing the correlation strength (Pearson’s correlation) between child and caregiver microbiomes for each family. Bubble size indicates the –log( P value), reflecting statistical significance, while bubble color corresponds to whether each family falls into the high‐ (violet) or low‐similarity (green) group. ( C ) Box plots depicting two alpha diversity metrics (Faith’s phylogenetic diversity and observed features, i.e., ASV richness) for pediatric samples in the high‐ and low‐similarity groups. ( D ) Differential abundance analysis using DESeq2, comparing high‐ (violet) versus low‐similarity (green) groups. Significantly differentially abundant ASVs (|Log2FoldChange| > 1, FDR < 0.05) are listed by taxonomic affiliation alongside the number of ASVs per taxon. Blue‐highlighted species names indicate >99% sequence identity to entries in the NCBI 16S rRNA database, confirming species‐level identification. In the bubble plot, circle size represents –log10(FDR), and color indicates the similarity group in which the ASV is enriched.

Article Snippet: To establish a standardized 16S rRNA sequencing analysis pipeline, five replicates of mock microbial DNA standards were analyzed using QIIME2, benchmarked against IR and the theoretical Zymo mock composition ( ).

Techniques: Sequencing