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TagGD: Fast and Accurate Software for DNA Tag Generation and Demultiplexing

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  • Paul Igor Costea
  • Joakim Lundeberg
  • Pelin Akan

Abstract

Multiplexing is of vital importance for utilizing the full potential of next generation sequencing technologies. We here report TagGD (DNA-based Tag Generator and Demultiplexor), a fully-customisable, fast and accurate software package that can generate thousands of barcodes satisfying user-defined constraints and can guarantee full demultiplexing accuracy. The barcodes are designed to minimise their interference with the experiment. Insertion, deletion and substitution events are considered when designing and demultiplexing barcodes. 20,000 barcodes of length 18 were designed in 5 minutes and 2 million barcoded Illumina HiSeq-like reads generated with an error rate of 2% were demultiplexed with full accuracy in 5 minutes. We believe that our software meets a central demand in the current high-throughput biology and can be utilised in any field with ample sample abundance. The software is available on GitHub (https://github.com/pelinakan/UBD.git).

Suggested Citation

  • Paul Igor Costea & Joakim Lundeberg & Pelin Akan, 2013. "TagGD: Fast and Accurate Software for DNA Tag Generation and Demultiplexing," PLOS ONE, Public Library of Science, vol. 8(3), pages 1-5, March.
    • Handle: RePEc:plo:pone00:0057521
    DOI: 10.1371/journal.pone.0057521
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    Cited by:

    1. S. Vickovic & B. Lötstedt & J. Klughammer & S. Mages & Å Segerstolpe & O. Rozenblatt-Rosen & A. Regev, 2022. "SM-Omics is an automated platform for high-throughput spatial multi-omics," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Alma Andersson & Ludvig Larsson & Linnea Stenbeck & Fredrik Salmén & Anna Ehinger & Sunny Z. Wu & Ghamdan Al-Eryani & Daniel Roden & Alex Swarbrick & Åke Borg & Jonas Frisén & Camilla Engblom & Joakim, 2021. "Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions," Nature Communications, Nature, vol. 12(1), pages 1-14, December.
    3. Bin Wang & Xiaopeng Wei & Jing Dong & Qiang Zhang, 2015. "Improved Lower Bounds of DNA Tags Based on a Modified Genetic Algorithm," PLOS ONE, Public Library of Science, vol. 10(2), pages 1-10, February.

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