2024 / 05

DOI: 10.24075/brsmu.2024.040

METHOD

Designing of custom barcodes for sequencing on the MGI platform

Shmitko AO, Bulusheva IA, Vasiliadis YuA, Suchalko ON, Syrko DS, Belova VA, Pavlova AS, Korostin DO
About authors

Pirogov Russian National Research Medical University

Correspondence should be addressed: Аnna O. Shmitko
Ostrovityanova, 1/1, Мoscow, 117997, Russia; moc.liamg@79imhsanna

About paper

Funding: this research was funded by the grant №075-15-2019-1789 from the Ministry of Science and Higher Education of the Russian Federation allocated to the Center for Precision Genome Editing and Genetic Technologies for Biomedicine.

Author contribution: Shmitko AO — study planning, data collection, writing Original Draft Preparation; Bulusheva IA — methodology, data analysis, writing Original Draft Preparation; Vasiliadis IA, Suchalko ON, Syrko DS — data analysis, software, visualization; Belova VA — study planning, manuscript review and editing; Pavlova AS — data curation, data analysis, software; Korostin DO — conceptualization, supervision, methodology, manuscript review and editing.

Received: 2024-08-15 Accepted: 2024-09-17 Published online: 2024-10-10
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  1. Jeon SA, Park JL, Park SJ, Kim JH, Goh SH, Han JY, et al. Comparison between MGI and Illumina sequencing platforms for whole genome sequencing. Genes Genomics. 2021; 43: 713–24. DOI: 10.1007/s13258-021-01096-x.
  2. Kim HM, Jeon S, Chung O, Jun JH, Kim HS, Blazyte A, et al. Comparative analysis of 7 short-read sequencing platforms using the Korean Reference Genome: MGI and Illumina sequencing benchmark for whole-genome sequencing. Gigascience. 2021; 10. DOI: 10.1093/gigascience/giab014.
  3. Xu Y, Lin Z, Tang C, Tang Y, Cai Y, Zhong H, et al. A new massively parallel nanoball sequencing platform for whole exome research. BMC Bioinformatics. 2019; 20. DOI: 10.1186/s12859-019-2751-3.
  4. Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science (1979). 2010; 327: 78–81. DOI: 10.1126/science.1181498.
  5. Fadrosh DW, Ma B, Gajer P, Sengamalay N, Ott S, Brotman RM, et al. An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform. 2014. Available from: http://www.microbiomejournal.com/content/2/1/6.
  6. Baym M, Kryazhimskiy S, Lieberman TD, Chung H, Desai MM, Kishony RK. Inexpensive multiplexed library preparation for megabase-sized genomes. PLoS One. 2015; 10. DOI: 10.1371/journal.pone.0128036.
  7. Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the miseq illumina sequencing platform. Appl Environ Microbiol. 2013; 79: 5112–20. DOI: 10.1128/AEM.01043-13.
  8. Bulusheva I, Belova V, Nikashin B, Korostin D. BC-store: A program for MGISEQ barcode sets analysis. PLoS One. 2021; 16. DOI: 10.1371/journal.pone.0247532.
  9. Faircloth BC, Glenn TC. Not all sequence tags are created equal: Designing and validating sequence identification tags robust to indels. PLoS One. 2012; 7. DOI: 10.1371/journal.pone.0042543.
  10. Trébeau C, De Monvel JB, Tai FWJ, Petit C, Etournay R. DNA Barcode Compatibility: An R-package for optimizing DNA-barcode combinations in multiplex sequencing experiments. Bioinformatics. 2019; 35: 2690–1. DOI: 10.1093/bioinformatics/bty1030.
  11. Varet H, Coppée JY. CheckMyIndex: A web-based R/ Shiny interface for choosing compatible sequencing indexes. Bioinformatics. 2019; 35: 901–2. DOI: 10.1093/bioinformatics/bty706.
  12. Oligos and primers for BGISEQ/DNBSEQ/MGISEQ - MGI Tech. Available from: https://en.mgitech.cn/Download/download_file/id/71.
  13. SureSelectXT HS Target Enrichment System For Illumina Multiplexed Sequencing Platforms, Version D1, July 2021. Available from: https://www.agilent.com/cs/library/usermanuals/public/G7530-90000.pdf.
  14. Li Q, Zhao X, Zhang W, Wang L, Wang J, Xu D, et al. Reliable multiplex sequencing with rare index mis-assignment on DNB-based NGS platform. BMC Genomics. 2019; 20. DOI: 10.1186/s12864-019-5569-5.