ArticleBMC bioinformatics2026
Benchmarking DNA barcode decoding strategies under high error rates.
Article in BMC bioinformatics, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
backgroundDNA barcoding enables multiplexed identification of biomolecules in pooled sequencing experiments, with broad applications including spatial transcriptomics. Photolithographic synthesis of high-density barcode arrays achieves library sizes exceeding [Formula: see text] unique sequences but introduces error rates of 10-20% per nucleotide through substitutions, insertions, and deletions. Classical error-correcting codes cannot scale to such library sizes while maintaining robust error correction under these conditions.
methodsWe benchmarked three computational barcode decoding approaches-Columba (FM-index-based lossless alignment), QUIK (k-mer filtering with GPU acceleration), and RandomBarcodes (trimer-based triage with GPU parallelization)-across simulated and empirical datasets. Simulations spanned barcode lengths of 28-36 nt, library sizes of 21,000-85,000 barcodes, and error rates of 9-32%. Real sequencing data were generated from photolithographically synthesized arrays at three printing density levels.
resultsUnder medium error rates (~23%), QUIK achieved the highest recall (87-89%) while maintaining precision [Formula: see text], outperforming RandomBarcodes (recall 56%, precision [Formula: see text]) and Columba (recall 35%, precision 98-100%). QUIK demonstrated superior scalability, processing 59,620 reads/second on a single GPU compared to RandomBarcodes (68 reads/second) and Columba (1550 reads/second with 8 CPU threads). Barcode length strongly influenced accuracy: 34-nt barcodes enabled 75% recall at 99.97% precision with QUIK, compared to 60% recall with 32-nt barcodes. On real data from a 42,000-spot subarray with 36-nt barcodes, QUIK managed a 57% assignment rate with perfect precision, versus 52% (Columba, precision 99.96) and 50% (RandomBarcodes, precision 99.82).
conclusionsQUIK provides the optimal balance of speed, accuracy, and scalability for high-density spatial transcriptomics applications under realistic synthesis error conditions. Barcode lengths [Formula: see text] nt are recommended for applications requiring [Formula: see text] read recovery at [Formula: see text] precision.
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