Accurate estimation of molecular counts from amplicon sequence data with unique molecular identifiers.

ABSTRACT:

Motivation

Amplicon sequencing is widely applied to explore heterogeneity and rare variants in genetic populations. 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. One solution attaches unique molecular identifiers (UMIs) to sample sequences before amplification. Counting UMIs instead of sequences provides unbiased estimates of abundance. While modern methods improve over naïve counting by UMI identity, most do not account for UMI reuse or collision, and they do not adequately model PCR and sequencing errors in the UMIs and sample sequences.

Results

We introduce Deduplicatio

SUBMITTER: Peng X 

PROVIDER: S-EPMC9891248 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature