Nov 11, 2020 · We propose AmpliCI, a likelihood-based denoiser of Illumina amplicon sequence data under the mixture model framework. We have shown that AmpliCI is better than three other popular denoising methods on most performance metrics, and retains acceptable computation time and memory usage.

AmpliCI, Amplicon Clustering Inference, denoises Illumina amplicon data by approximate model-based clustering. AmpliCI v2.0 now incorporates our new Unique Molecular Identifier (UMI)-aware software DAUMI to denoise UMI-tagged Illumina amplicon sequences.

Jul 22, 2020 · Results: We introduce AmpliCI, a reference-free, model-based method for rapidly resolving the number, abundance and identity of error-free sequences in massive Illumina amplicon datasets....

Feb 23, 2020 · Motivation: Next-generation amplicon sequencing is a powerful tool for investigating microbial commu-nities. One main challenge is to distinguish true biological variants from errors caused by PCR and sequencing.

DAUMI greatly enhances the accuracy of detecting rare sequences and provides deduplicated abundance estimation, eliminating sequencing errors, many PCR errors and PCR bias. DAUMI is part of the AmpliCI software. Please check the AmpliCI instructions for installation.

Jan 5, 2023 · Resolving true biological variants and quantifying their abundance is crucial for downstream analyses, but measured abundances are distorted by stochasticity and bias in amplification, plus errors during polymerase chain reaction (PCR) and sequencing.

DAUMI (AmpliCI-UMI), Amplicon Clustering Inference with UMI information, is built on AmpliCI, but takes advantage of UMI information for denoising amplicon sequencing data, which contributes to a more accurate error profile and better clustering results.

Basic PCR is commonplace in many molecular biology labs where it is used to amplify DNA fragments and detect DNA or RNA sequences within a cell or environment. However, PCR has evolved far beyond simple amplification and detection, and many extensions of the original PCR method have been described.

PCR amplification is a known method to get multiple copies (thousand to million) of a desired DNA sequence of the DNA template via the process of thermal cycling. Here, the definition, setup, steps, advantages and limitations of the polymerase chain reaction have been explained.

Feb 25, 2020 · High-throughput sequencing of 16S ribosomal RNA gene amplicons has facilitated understanding of complex microbial communities, but the inherent noise in PCR and DNA sequencing limits ...