Article

URAdime – a tool for analyzing primer sequences in sequencing data to identify dimers and super-amplicons

2025-01-28

Abstract excerpt

Targeted sequencing of multiplex PCR amplicons is commonplace in research laboratories and clinical diagnostics. There are numerous tools for the a priori optimization of primers and reactions, but no tools to detect specific problematic primers post hoc. We developed URAdime, a tool for analyzing primer sequences in sequencing data to identify dimers and super-amplicons. We show that it successfully detects these...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 00b084fb-975b-58d5-abdb-dfcc458f384a
DOI: 10.1101/2025.01.25.634870

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

URAdime – a tool for analyzing primer sequences in sequencing data to identify dimers and super-ampliconsDOI 10.1101/2025.01.25.634870Read

Minor variant detection in amplicons using 454 massive parallel pyrosequencing: experiences and considerations for successful applications.Semantic proximity Read

Scaling Multiplex qPCR Primer Design to 1000-plex using the Degenerate Incomplete Multiplex Primer List Extension (DIMPLE) AlgorithmSemantic proximity Read

PCR-SSP: a cautionary tale and an update of the Bein primer mixes.Semantic proximity Read

MultiPrime: A Reliable and Efficient Tool for Targeted Next-Generation SequencingSemantic proximity Read

PrimerMapper: high throughput primer design and graphical assembly for PCR and SNP detection.Semantic proximity Read

CalcDalton: a tool for multiplex genotyping primer design for single-base extension reactions using cleavable primers.Semantic proximity Read

RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation.Semantic proximity Read

In silico PCR analysis.Semantic proximity Read

primerJinn – a tool for rationally designing multiplex PCR primer sets and in silico PCRSemantic proximity Read

AmpSeqR: an R package for amplicon deep sequencing data analysisSemantic proximity Read

AmpSeqR: an R package for amplicon deep sequencing data analysisSemantic proximity Read

DFold: PCR design that minimizes secondary structure and optimizes downstream genotyping applications.Semantic proximity Read