ArticleProceedings of the National Academy of Sciences of the United States of America2018
Indel-correcting DNA barcodes for high-throughput sequencing.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- The diverse functions of viral microproteins.bioRxiv : the preprint server for biology · 2026Article
- Single-cell genomics links targeted functional manipulations to efficacy-associated chromatin signatures in CAR T cells.Research square · 2026Article
- Benchmarking DNA barcode decoding strategies under high error rates.BMC bioinformatics · 2026Article
- From spacecraft ranging to massive DNA data storage: Composite ranging codes as indices and error correction references.Science advances · 2026Article
- A set of genetic tools for use inMicrobiology (Reading, England) · 2026Article
- Fast barcode calling based onPNAS nexus · 2026Article
- Scaling perturbations: beyond genome-scale CRISPR screens.bioRxiv : the preprint server for biology · 2026Article
- Generative Design of Cell Type-Specific RNA Splicing Elements for Programmable Gene Regulation.bioRxiv : the preprint server for biology · 2025Article
- Functional phenotyping of genomic variants using joint multiomic single-cell DNA-RNA sequencing.Nature methods · 2025Article
- Self-documenting plasmids.Trends in biotechnology · 2025Review
- A Reverse Transcription Nucleic-Acid-Based Barcoding System forACS bio & med chem Au · 2025Article
- Automated Design of Oligopools and Rapid Analysis of Massively Parallel Barcoded Measurements.ACS synthetic biology · 2024Article
- TDFPS-Designer: an efficient toolkit for barcode design and selection in nanopore sequencing.Genome biology · 2024Article
- Cryptographic approaches to authenticating synthetic DNA sequences.Trends in biotechnology · 2024Review
- Article
- Generating barcodes for nanopore sequencing data with PRO.Fundamental research · 2024Article
- Article
- Decoding the complexity of on-target integration: characterizing DNA insertions at the CRISPR-Cas9 targeted locus using nanopore sequencing.BMC genomics · 2024Article
- Highly Accurate Sequence- and Position-Independent Error Profiling of DNA Synthesis and Sequencing.ACS synthetic biology · 2023Article
- GREPore-seq: A Robust Workflow to Detect Changes After Gene Editing Through Long-range PCR and Nanopore Sequencing.Genomics, proteomics & bioinformatics · 2023Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Many large-scale, high-throughput experiments use DNA barcodes, short DNA sequences prepended to DNA libraries, for identification of individuals in pooled biomolecule populations. However, DNA synthesis and sequencing errors confound the correct interpretation of observed barcodes and can lead to significant data loss or spurious results. Widely used error-correcting codes borrowed from computer science (e.g., Hamming, Levenshtein codes) do not properly account for insertions and deletions (indels) in DNA barcodes, even though deletions are the most common type of synthesis error. Here, we present and experimentally validate filled/truncated right end edit (FREE) barcodes, which correct substitution, insertion, and deletion errors, even when these errors alter the barcode length. FREE barcodes are designed with experimental considerations in mind, including balanced guanine-cytosine (GC) content, minimal homopolymer runs, and reduced internal hairpin propensity. We generate and include lists of barcodes with different lengths and error correction levels that may be useful in diverse high-throughput applications, including >10
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