ArticleFrontiers in genetics2021
UMIc: A Preprocessing Method for UMI Deduplication and Reads Correction.
Article in Frontiers in genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Unique molecular identifiers don't need to be unique: a collision-aware estimator for RNA-seq quantification.bioRxiv : the preprint server for biology · 2026Article
- umite: fast quantification of Smart-seq3 libraries with improved UMI retrieval.Bioinformatics (Oxford, England) · 2026Article
- piRNAs safeguard splicing and RNA fidelity during heat shock.bioRxiv : the preprint server for biology · 2025Article
- Evaluation of false positive and false negative errors in targeted next generation sequencing.Genome biology · 2025Article
- fastp 1.0: An ultra-fast all-round tool for FASTQ data quality control and preprocessing.iMeta · 2025Article
- How error correction affects polymerase chain reaction deduplication: A survey based on unique molecular identifier datasets of short reads.Quantitative biology (Beijing, China) · 2025Review
- Early Detection, Precision Treatment, Recurrence Monitoring: Liquid Biopsy Transforms Colorectal Cancer Therapy.Current cancer drug targets · 2025Review
- Construction of edit-distance graphs for large sets of short reads through minimizer-bucketing.Bioinformatics advances · 2025Article
- Correcting PCR amplification errors in unique molecular identifiers to generate accurate numbers of sequencing molecules.Nature methods · 2024Article
- A cost-effective sequencing method for genetic studies combining high-depth whole exome and low-depth whole genome.NPJ genomic medicine · 2024Article
- Genetic Diversity Assessment in Plants from Reduced Representation Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Identification of Novel Induced Mutations in Seed and Vegetatively Propagated Plants from Reduced Representation or Whole Genome Sequencing Data.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Circulating tumor DNA in early-stage colon cancer: ready for prime time or needing refinement?Therapeutic advances in medical oncology · 2022Review
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A recent refinement in high-throughput sequencing involves the incorporation of unique molecular identifiers (UMIs), which are random oligonucleotide barcodes, on the library preparation steps. A UMI adds a unique identity to different DNA/RNA input molecules through polymerase chain reaction (PCR) amplification, thus reducing bias of this step. Here, we propose an alignment free framework serving as a preprocessing step of fastq files, called UMIc, for deduplication and correction of reads building consensus sequences from each UMI. Our approach takes into account the frequency and the Phred quality of nucleotides and the distances between the UMIs and the actual sequences. We have tested the tool using different scenarios of UMI-tagged library data, having in mind the aspect of a wide application. UMIc is an open-source tool implemented in R and is freely available from https://github.com/BiodataAnalysisGroup/UMIc.
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