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AmpliFuse workflow and representative chimera formations with alignment analyses. ( A ) Overview of the AmpliFuse workflow. ( B and C ) Schematic of representative chimera formations using datasets derived from ZymoBIOMICS <t>16S</t> <t>V3–V4</t> mock community ( B ) and the AMR panel ( C ). The expected breakpoint (dashed line) lies within a microhomology (MH) highlighted in yellow. ( D and E ) Example alignments of two parent amplicons to a representative chimeric amplicon generated from the ZymoBIOMICS ( D ) and AMR panel ( E ) datasets, respectively. Under the default settings, chimeric amplicons account for approximately 15.4 and 4.9% of all amplicons generated using the ZymoBIOMICS and the AMR panel datasets, respectively.
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AmpliFuse workflow and representative chimera formations with alignment analyses. ( A ) Overview of the AmpliFuse workflow. ( B and C ) Schematic of representative chimera formations using datasets derived from ZymoBIOMICS <t>16S</t> <t>V3–V4</t> mock community ( B ) and the AMR panel ( C ). The expected breakpoint (dashed line) lies within a microhomology (MH) highlighted in yellow. ( D and E ) Example alignments of two parent amplicons to a representative chimeric amplicon generated from the ZymoBIOMICS ( D ) and AMR panel ( E ) datasets, respectively. Under the default settings, chimeric amplicons account for approximately 15.4 and 4.9% of all amplicons generated using the ZymoBIOMICS and the AMR panel datasets, respectively.
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AmpliFuse workflow and representative chimera formations with alignment analyses. ( A ) Overview of the AmpliFuse workflow. ( B and C ) Schematic of representative chimera formations using datasets derived from ZymoBIOMICS <t>16S</t> <t>V3–V4</t> mock community ( B ) and the AMR panel ( C ). The expected breakpoint (dashed line) lies within a microhomology (MH) highlighted in yellow. ( D and E ) Example alignments of two parent amplicons to a representative chimeric amplicon generated from the ZymoBIOMICS ( D ) and AMR panel ( E ) datasets, respectively. Under the default settings, chimeric amplicons account for approximately 15.4 and 4.9% of all amplicons generated using the ZymoBIOMICS and the AMR panel datasets, respectively.
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AmpliFuse workflow and representative chimera formations with alignment analyses. ( A ) Overview of the AmpliFuse workflow. ( B and C ) Schematic of representative chimera formations using datasets derived from ZymoBIOMICS <t>16S</t> <t>V3–V4</t> mock community ( B ) and the AMR panel ( C ). The expected breakpoint (dashed line) lies within a microhomology (MH) highlighted in yellow. ( D and E ) Example alignments of two parent amplicons to a representative chimeric amplicon generated from the ZymoBIOMICS ( D ) and AMR panel ( E ) datasets, respectively. Under the default settings, chimeric amplicons account for approximately 15.4 and 4.9% of all amplicons generated using the ZymoBIOMICS and the AMR panel datasets, respectively.
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AmpliFuse workflow and representative chimera formations with alignment analyses. ( A ) Overview of the AmpliFuse workflow. ( B and C ) Schematic of representative chimera formations using datasets derived from ZymoBIOMICS <t>16S</t> <t>V3–V4</t> mock community ( B ) and the AMR panel ( C ). The expected breakpoint (dashed line) lies within a microhomology (MH) highlighted in yellow. ( D and E ) Example alignments of two parent amplicons to a representative chimeric amplicon generated from the ZymoBIOMICS ( D ) and AMR panel ( E ) datasets, respectively. Under the default settings, chimeric amplicons account for approximately 15.4 and 4.9% of all amplicons generated using the ZymoBIOMICS and the AMR panel datasets, respectively.
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AmpliFuse workflow and representative chimera formations with alignment analyses. ( A ) Overview of the AmpliFuse workflow. ( B and C ) Schematic of representative chimera formations using datasets derived from ZymoBIOMICS 16S V3–V4 mock community ( B ) and the AMR panel ( C ). The expected breakpoint (dashed line) lies within a microhomology (MH) highlighted in yellow. ( D and E ) Example alignments of two parent amplicons to a representative chimeric amplicon generated from the ZymoBIOMICS ( D ) and AMR panel ( E ) datasets, respectively. Under the default settings, chimeric amplicons account for approximately 15.4 and 4.9% of all amplicons generated using the ZymoBIOMICS and the AMR panel datasets, respectively.

Journal: Microbiology Resource Announcements

Article Title: AmpliFuse: an amplicon simulation tool with enhanced chimera generation for Illumina platforms

doi: 10.1128/mra.01439-25

Figure Lengend Snippet: AmpliFuse workflow and representative chimera formations with alignment analyses. ( A ) Overview of the AmpliFuse workflow. ( B and C ) Schematic of representative chimera formations using datasets derived from ZymoBIOMICS 16S V3–V4 mock community ( B ) and the AMR panel ( C ). The expected breakpoint (dashed line) lies within a microhomology (MH) highlighted in yellow. ( D and E ) Example alignments of two parent amplicons to a representative chimeric amplicon generated from the ZymoBIOMICS ( D ) and AMR panel ( E ) datasets, respectively. Under the default settings, chimeric amplicons account for approximately 15.4 and 4.9% of all amplicons generated using the ZymoBIOMICS and the AMR panel datasets, respectively.

Article Snippet: AmpliFuse was demonstrated utilizing two publicly available datasets, namely, ZymoBIOMICS Microbial Community ( https://zymoresearch.eu/collections/zymobiomics-microbial-community-standards/products/zymobiomics-microbial-community-standard ) using 16S rRNA gene V3–V4 primer pairs (341F and 805R) ( ) and the Illumina AmpliSeq AMR Research Panel (the AMR panel) ( https://www.illumina.com/products/by-brand/ampliseq/community-panels/antimicrobial-resistance.html ).

Techniques: Derivative Assay, Amplification, Generated