{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,18]],"date-time":"2026-04-18T04:35:25Z","timestamp":1776486925247,"version":"3.51.2"},"reference-count":29,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,12,12]],"date-time":"2024-12-12T00:00:00Z","timestamp":1733961600000},"content-version":"vor","delay-in-days":20,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["81930056"],"award-info":[{"award-number":["81930056"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32370669"],"award-info":[{"award-number":["32370669"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Short tandem repeats (STRs) represent one of the most polymorphic variations in the human genome, finding extensive applications in forensics, population genetics and medical genetics. In contrast to the traditional capillary electrophoresis (CE) method, genotyping STRs using massive parallel sequencing technology offers enhanced sensitivity and accuracy. However, current methods are mainly designed for target sequencing with higher coverage for a specific STR locus, thereby constraining the utility of STRs in low- and medium-coverage whole genome sequencing (WGS) data. Here, we introduce STRsensor, a method designed to type STR alleles in low-coverage WGS data and target sequencing data, achieving a significant high detection ratio and accuracy. STRsensor employs two methods for STR allele-typing: the Kmers-based method and the CIGAR-based method. Furthermore, by incorporating a model for PCR stutters, STRsensor greatly enhances the accuracy of STR allele typing. With simulation data, we demonstrate that STRsensor achieves a detection ratio of 100$\\%$ and an accuracy of 99.37$\\%$ for a 30$\\times $ WGS data, outperforming the existing methods, such as STRait Razor, STRinNGS, and HipSTR. When applied to real target sequencing data from 687 individuals, STRsensor achieves a detection ratio of 99.64$\\%$ and an accuracy of 99.99$\\%$. Moreover, STRsensor is a computationally efficient method that runs 79 times faster than HipSTR and 10 000 times faster than STRinNGS. STRsensor is freely available on GitHub: https:\/\/github.com\/ChenHuaLab\/STRsensor.<\/jats:p>","DOI":"10.1093\/bib\/bbae637","type":"journal-article","created":{"date-parts":[[2024,12,12]],"date-time":"2024-12-12T12:22:03Z","timestamp":1734006123000},"source":"Crossref","is-referenced-by-count":1,"title":["STRsensor: a computationally efficient method for STR allele-typing from massively parallel sequencing data"],"prefix":"10.1093","volume":"26","author":[{"given":"Xiaolong","family":"Zhang","sequence":"first","affiliation":[{"name":"Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101 ,","place":["China"]},{"name":"School of Future Technology, University of Chinese Academy of Sciences , Beijing 100049 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xianchao","family":"Ji","sequence":"additional","affiliation":[{"name":"Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101 ,","place":["China"]},{"name":"School of Future Technology, University of Chinese Academy of Sciences , Beijing 100049 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lingxiang","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Archaeological Science, Fudan University , Shanghai 200032 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lianjiang","family":"Chi","sequence":"additional","affiliation":[{"name":"Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chengtao","family":"Li","sequence":"additional","affiliation":[{"name":"Shanghai Medical College, Fudan University , Shanghai 200032 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shaoqing","family":"Wen","sequence":"additional","affiliation":[{"name":"Institute of Archaeological Science, Fudan University , Shanghai 200032 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hua","family":"Chen","sequence":"additional","affiliation":[{"name":"Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation , Beijing 100101 ,","place":["China"]},{"name":"School of Future Technology, University of Chinese Academy of Sciences , Beijing 100049 ,","place":["China"]},{"name":"CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming 650023 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,12,12]]},"reference":[{"key":"2024121212215580100_ref1","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1016\/j.fsigen.2013.04.005","article-title":"STRait razor: a length-based forensic STR allele-calling tool for use with second generation sequencing data","volume":"7","author":"Warshauer","year":"2013","journal-title":"Forensic Sci Int Genet"},{"key":"2024121212215580100_ref2","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1016\/j.fsigen.2015.02.002","article-title":"Next generation sequencing and its applications in forensic genetics","volume":"18","author":"Borsting","year":"2015","journal-title":"Forensic Sci Int Genet"},{"key":"2024121212215580100_ref3","doi-asserted-by":"publisher","first-page":"1154","DOI":"10.1101\/gr.135780.111","article-title":"lobSTR: a short tandem repeat profiler for personal genomes","volume":"22","author":"Gymrek","year":"2012","journal-title":"Genome Res"},{"key":"2024121212215580100_ref4","volume-title":"Handbook of Statistical Genetics","author":"Balding","year":"2001"},{"key":"2024121212215580100_ref5","doi-asserted-by":"publisher","first-page":"590","DOI":"10.1038\/nmeth.4267","article-title":"Genome-wide profiling of heritable and de novo STR variations","volume":"14","author":"Willems","year":"2017","journal-title":"Nat Methods"},{"key":"2024121212215580100_ref6","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1146\/annurev-genet-072610-155046","article-title":"Variable tandem repeats accelerate evolution of coding and regulatory sequences","volume":"44","author":"Gemayel","year":"2010","journal-title":"Annu Rev Genet"},{"key":"2024121212215580100_ref7","doi-asserted-by":"publisher","first-page":"991","DOI":"10.1093\/molbev\/msh073","article-title":"Microsatellites within genes: structure, function, and evolution","volume":"21","author":"Li","year":"2004","journal-title":"Mol Biol Evol"},{"key":"2024121212215580100_ref8","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1111\/j.1556-4029.2006.00046.x","article-title":"Genetics and genomics of core short tandem repeat loci used in human identity testing","volume":"51","author":"Butler","year":"2006","journal-title":"J Forensic Sci"},{"key":"2024121212215580100_ref9","doi-asserted-by":"publisher","first-page":"190","DOI":"10.1016\/j.gpb.2014.09.001","article-title":"Application of next-generation sequencing technology in forensic science","volume":"12","author":"Yang","year":"2014","journal-title":"Genom Proteom Bioinform"},{"key":"2024121212215580100_ref10","doi-asserted-by":"publisher","first-page":"66","DOI":"10.1016\/j.fsigen.2017.11.014","article-title":"Inferring Chinese surnames with Y-STR profiles","volume":"33","author":"Shi","year":"2018","journal-title":"Forensic Sci Int: Genet"},{"key":"2024121212215580100_ref11","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1038\/nrg2952","article-title":"Improving human forensics through advances in genetics, genomics and molecular biology","volume":"12","author":"Kayser","year":"2011","journal-title":"Nat Rev Genet"},{"key":"2024121212215580100_ref12","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1007\/978-1-61779-461-2_1","article-title":"An overview of DNA typing methods for human identification: past, present, and future","volume":"830","author":"Thompson","year":"2012","journal-title":"Methods Mol Biol"},{"key":"2024121212215580100_ref13","doi-asserted-by":"publisher","first-page":"1692","DOI":"10.1111\/1556-4029.13767","article-title":"Massively parallel sequencing of forensic STRs using the ion chef and the ion S5 XL systems","volume":"63","author":"Wang","year":"2018","journal-title":"J Forensic Sci"},{"key":"2024121212215580100_ref14","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1016\/j.fsigen.2015.07.015","article-title":"An evaluation of the PowerSeq auto system: a multiplex short tandem repeat marker kit compatible with massively parallel sequencing","volume":"19","author":"Zeng","year":"2015","journal-title":"Forensic Sci Int Genet"},{"key":"2024121212215580100_ref15","doi-asserted-by":"publisher","first-page":"810","DOI":"10.1016\/j.fsigen.2012.03.004","article-title":"Forensic STR analysis using massive parallel sequencing","volume":"6","author":"Van Neste","year":"2012","journal-title":"Forensic Sci Int Genet"},{"key":"2024121212215580100_ref16","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1016\/j.fsigen.2012.02.002","article-title":"Automated analysis of sequence polymorphism in STR alleles by PCR and direct electrospray ionization mass spectrometry","volume":"6","author":"Planz","year":"2012","journal-title":"Forensic Sci Int Genet"},{"key":"2024121212215580100_ref17","doi-asserted-by":"publisher","first-page":"2012","DOI":"10.2144\/000113857","article-title":"Short-read, high-throughput sequencing technology for STR genotyping","volume":"1\u20136","author":"Bornman","year":"2012","journal-title":"Biotech Rapid Dispatches"},{"key":"2024121212215580100_ref18","doi-asserted-by":"publisher","first-page":"127","DOI":"10.2144\/000113721","article-title":"High-throughput sequencing of core STR loci for forensic genetic investigations using the Roche genome sequencer FLX platform","volume":"51","author":"Fordyce","year":"2011","journal-title":"Biotechniques"},{"key":"2024121212215580100_ref19","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1016\/j.fsigen.2014.10.011","article-title":"STRait razor v2.0: the improved STR allele identification tool \u2013 Razor","volume":"14","author":"Warshauer","year":"2015","journal-title":"Forensic Sci Int Genet"},{"key":"2024121212215580100_ref20","doi-asserted-by":"publisher","first-page":"102331","DOI":"10.1016\/j.fsigen.2020.102331","article-title":"STRinNGS v2.0: improved tool for analysis and reporting of STR sequencing data","volume":"48","author":"Jonck","year":"2020","journal-title":"Forensic Sci Int Genet"},{"key":"2024121212215580100_ref21","doi-asserted-by":"publisher","first-page":"135","DOI":"10.1016\/j.fsigen.2017.09.003","article-title":"Massively parallel sequencing of forensic STRs and SNPs using the Illumina$\\circledR $ ForenSeq$^TM$ DNA signature prep kit on the MiSeq FGx$^TM$ forensic genomics system","volume":"31","author":"Guo","year":"2017","journal-title":"Forensic Sci Int: Genet"},{"key":"2024121212215580100_ref22","doi-asserted-by":"publisher","first-page":"6810","DOI":"10.1038\/s41598-018-24495-9","article-title":"Sequence investigation of 34 forensic autosomal STRs with massively parallel sequencing","volume":"8","author":"Zhang","year":"2018","journal-title":"Sci Rep"},{"key":"2024121212215580100_ref23","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1186\/s12859-017-1800-z","article-title":"STRScan: Targeted profiling of short tandem repeats in whole-genome sequencing data","volume":"18","author":"Tang","year":"2017","journal-title":"BMC bioinformatics"},{"key":"2024121212215580100_ref24","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1186\/s13059-022-02826-4","article-title":"STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci","volume":"23","author":"Dashnow","year":"2022","journal-title":"Genome Biol"},{"key":"2024121212215580100_ref25","doi-asserted-by":"publisher","first-page":"4754","DOI":"10.1093\/bioinformatics\/btz431","article-title":"ExpansionHunter: a sequence-graph-based tool to analyze variation in short tandem repeat regions","volume":"35","author":"Dolzhenko","year":"2019","journal-title":"Bioinformatics"},{"key":"2024121212215580100_ref26","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1186\/s12859-019-2854-x","article-title":"pTrimmer: an efficient tool to trim primers of multiplex deep sequencing data","volume":"20","author":"Zhang","year":"2019","journal-title":"BMC Bioinform"},{"key":"2024121212215580100_ref27","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2024121212215580100_ref28","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1016\/j.gpb.2020.02.001","article-title":"MSIsensor-pro: fast, accurate, and matched-normal-sample-free detection of microsatellite instability","volume":"18","author":"Jia","year":"2020","journal-title":"Genom Proteom Bioinform"},{"key":"2024121212215580100_ref29","doi-asserted-by":"publisher","first-page":"1841","DOI":"10.1109\/TCBB.2019.2955081","article-title":"Alignment-free sequence comparison with multiple k values","volume":"18","author":"Ying Qian","year":"2021","journal-title":"IEEE\/ACM Trans Comput Biol Bioinform"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/1\/bbae637\/61085318\/bbae637.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/1\/bbae637\/61085318\/bbae637.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,12]],"date-time":"2024-12-12T12:22:19Z","timestamp":1734006139000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbae637\/7922198"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,11,22]]},"references-count":29,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,11,22]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbae637","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,1]]},"published":{"date-parts":[[2024,11,22]]},"article-number":"bbae637"}}