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

TL;DR

AmpliFuse is a tool that simulates realistic amplicon datasets, including chimeric reads, to improve the evaluation of sequencing methods in microbiome and AMR research.

Contribution

AmpliFuse introduces a novel approach to simulate amplicon datasets with realistic chimeric reads for Illumina platforms.

Findings

AmpliFuse simulates realistic amplicon datasets using in silico PCR and chimera formation.

The tool generates biologically relevant chimeric reads to benchmark detection algorithms.

AmpliFuse supports improved evaluation of sequencing workflows in microbiome and AMR studies.

Abstract

PCR-generated chimeric amplicons undermine the accuracy and reliability of subsequent amplicon-sequencing analyses. AmpliFuse, a Python-based tool, simulates realistic amplicon datasets through in silico PCR, chimera formation, and read simulation. By providing biologically relevant chimera-containing amplicon reads, AmpliFuse would facilitate benchmarking of chimera-detection algorithms and workflows, advancing microbiome and AMR research.

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