MAUI-seq: Metabarcoding using amplicons with unique molecular
identifiers to improve error correction
Abstract
Background: Sequencing and PCR errors are a major challenge when
characterising genetic diversity using high-throughput amplicon
sequencing (HTAS). Results: We have developed a multiplexed HTAS method,
MAUI-seq, which uses unique molecular identifiers (UMIs) to improve
error correction by exploiting variation among sequences associated with
a single UMI. We show that two main advantages of this approach are
efficient elimination of chimeric and other erroneous reads,
outperforming DADA2 and UNOISE3, and the ability to confidently
recognise genuine alleles that are present at low abundance or resemble
chimeras. Conclusions: The method provides sensitive and flexible
profiling of diversity and is readily adaptable to most HTAS
applications, including microbial 16S rRNA profiling and metabarcoding
of environmental DNA.