{"id":28613,"date":"2023-06-24T01:22:06","date_gmt":"2023-06-23T23:22:06","guid":{"rendered":"https:\/\/kinit.sk\/publication\/warpstr-determining-tandem-repeat-lengths-using-raw-nanopore-signals\/"},"modified":"2026-04-23T15:16:16","modified_gmt":"2026-04-23T13:16:16","slug":"warpstr-determining-tandem-repeat-lengths-using-raw-nanopore-signals","status":"publish","type":"publication","link":"https:\/\/kinit.sk\/sk\/publikacia\/warpstr-determining-tandem-repeat-lengths-using-raw-nanopore-signals\/","title":{"rendered":"WarpSTR: Determining Tandem Repeat Lengths Using Raw Nanopore Signals"},"content":{"rendered":"
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Sitarcik, J.1,2,5<\/sup>, Vinar, T.3<\/sup>, Brejova, B.3<\/sup>, Krampl, W.1,2,4<\/sup>, Budi\u0161, J.1,2,5<\/sup>, Radvanszky, J.1,2,6<\/sup>, Lucka, M.<\/strong>3<\/strong><\/sup><\/p>\n<\/div>\n\n

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Short tandem repeats (STRs) are regions of a genome containing many consecutive copies of the same short motif, possibly with small variations. Analysis of STRs has many clinical uses, but is limited by technology mainly due to STRs surpassing the used read length. Nanopore sequencing, as one of long read sequencing technologies, produces very long reads, thus offering more possibilities to study and analyze STRs. Basecalling of nanopore reads is however particularly unreliable in repeating regions, and therefore direct analysis from raw nanopore data is required.
Here we present WarpSTR, a novel method for characterizing both simple and complex tandem repeats directly from raw nanopore signals using a finite-state automaton and a search algorithm analogous to dynamic time warping. By applying this approach to determine the lengths of 241 STRs, we demonstrate that our approach decreases the mean absolute error of the STR length estimate compared to basecalling and STRique.<\/p>\n<\/div>\n\n

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1<\/sup>Comenius University Science Park, Bratislava, Slovakia
2<\/sup>Geneton Ltd., Bratislava, Slovakia<\/em>
3<\/sup>Faculty of Mathematics, Physics, and Informatics, Comenius University, Bratislava, Slovakia<\/em>
4<\/sup>Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia<\/em>
5<\/sup>Slovak Centre of Scientific and Technical Information, Bratislava, Slovakia<\/em>
6<\/sup>Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, Bratislava, Slovakia<\/em><\/p>\n<\/div>\n\n

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Cite: Sitarcik, J., Vinar, T., Brejova, B., Krampl, W., Budi\u0161, J., Radvanszky, J., Lucka, M. WarpSTR: Determining Tandem Repeat Lengths Using Raw Nanopore Signals. Bioinformatics (2023). DOI: 10.1093\/bioinformatics\/btad388<\/a><\/p>\n<\/div>\n\n\n","protected":false},"featured_media":0,"template":"","meta":{"_acf_changed":false,"footnotes":""},"categories":[81,142],"class_list":["post-28613","publication","type-publication","status-publish","hentry","category-data-analytics-for-green-energy-sk","category-2023-sk"],"acf":[],"yoast_head":"\nWarpSTR: Determining Tandem Repeat Lengths Using Raw Nanopore Signals - KInIT<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/kinit.sk\/sk\/publikacia\/warpstr-determining-tandem-repeat-lengths-using-raw-nanopore-signals\/\" \/>\n<meta property=\"og:locale\" content=\"sk_SK\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"WarpSTR: Determining Tandem Repeat Lengths Using Raw Nanopore Signals - KInIT\" \/>\n<meta property=\"og:description\" content=\"Sitarcik, J.1,2,5, Vinar, T.3, Brejova, B.3, Krampl, W.1,2,4, Budi\u0161, J.1,2,5, Radvanszky, J.1,2,6, Lucka, M.3 Short tandem repeats (STRs) are regions of a genome containing many consecutive copies of the same...\" \/>\n<meta property=\"og:url\" content=\"https:\/\/kinit.sk\/sk\/publikacia\/warpstr-determining-tandem-repeat-lengths-using-raw-nanopore-signals\/\" \/>\n<meta property=\"og:site_name\" content=\"KInIT\" \/>\n<meta property=\"article:modified_time\" content=\"2026-04-23T13:16:16+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/kinit.sk\/wp-content\/uploads\/2021\/03\/KINIT_Sharepic.png\" \/>\n\t<meta property=\"og:image:width\" content=\"1200\" \/>\n\t<meta property=\"og:image:height\" content=\"628\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/png\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:site\" content=\"@kinit\" \/>\n<meta name=\"twitter:label1\" content=\"Predpokladan\u00fd \u010das \u010d\u00edtania\" \/>\n\t<meta name=\"twitter:data1\" content=\"1 min\u00fata\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/kinit.sk\\\/sk\\\/publikacia\\\/warpstr-determining-tandem-repeat-lengths-using-raw-nanopore-signals\\\/\",\"url\":\"https:\\\/\\\/kinit.sk\\\/sk\\\/publikacia\\\/warpstr-determining-tandem-repeat-lengths-using-raw-nanopore-signals\\\/\",\"name\":\"WarpSTR: Determining Tandem Repeat Lengths Using Raw Nanopore Signals - 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