Paper Info
Title
AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing.
Abstract
Motivation: Unique molecular identifiers (UMIs) are added to DNA fragments before PCR amplification to discriminate between alleles arising from the same genomic locus and sequencing reads produced by PCR amplification. While computational methods have been developed to take into account UMI information in genome-wide and single-cell sequencing studies, they are not designed for modern amplicon-based sequencing experiments, especially in cases of high allelic diversity. Importantly, no guidelines are provided for the design of optimal UMI length for amplicon-based sequencing experiments. Results: Based on the total number of DNA fragments and the distribution of allele frequencies, we present a model for the determination of the minimum UMI length required to prevent UMI collisions and reduce allelic distortion. We also introduce a user-friendly software tool called AmpUMI to assist in the design and the analysis of UMI-based amplicon sequencing studies. AmpUMI provides quality control metrics on frequency and quality of UMIs, and trims and deduplicates amplicon sequences with user specified parameters for use in downstream analysis.
Year
DOI
Venue
2018
10.1093/bioinformatics/bty264
BIOINFORMATICS
Field
DocType
Volume
Software tool,Polymerase chain reaction,Allele,Biology,Identifier,Allele frequency,Amplicon,Locus (genetics),Genetics
Journal
34
Issue
ISSN
Citations 
13
1367-4803
0
PageRank 
References 
Authors
0.34
8
4
Name
Order
Citations
PageRank
Kendell Clement100.34
Rick Farouni200.68
Daniel Bauer301.35
Luca Pinello4497.71