ArticleBMC bioinformatics2017
STRScan: targeted profiling of short tandem repeats in whole-genome sequencing data.
Article in BMC bioinformatics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 20 citations in OpenAlex.
- A genome-wide approach for the discovery of novel repeat expansion disorders in the Undiagnosed Diseases Network cohort.Genetics in medicine : official journal of the American College of Medical Genetics · 2025Article
- STRsensor: a computationally efficient method for STR allele-typing from massively parallel sequencing data.Briefings in bioinformatics · 2024Article
- Review
- BigFiRSt: A Software Program Using Big Data Technique for Mining Simple Sequence Repeats From Large-Scale Sequencing Data.Frontiers in big data · 2021Article
- Large scale in silico characterization of repeat expansion variation in human genomes.Scientific data · 2020Article
- Article
- STRsearch: a new pipeline for targeted profiling of short tandem repeats in massively parallel sequencing data.Hereditas · 2020Article
- MultiplexSSR: A pipeline for developing multiplex SSR-PCR assays from resequencing data.Ecology and evolution · 2020Article
- Accuracy of short tandem repeats genotyping tools in whole exome sequencing data.F1000Research · 2020Article
- Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants.Molecules (Basel, Switzerland) · 2018Review
- The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools.BMC bioinformatics · 2017Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundShort tandem repeats (STRs) are found in many prokaryotic and eukaryotic genomes, and are commonly used as genetic markers, in particular for identity and parental testing in DNA forensics. The unstable expansion of some STRs was associated with various genetic disorders (e.g., the Huntington disease), and thus was used in genetic testing for screening individuals at high risk. Traditional STR analyses were based on the PCR amplification of STR loci followed by gel electrophoresis. With the availability of massive whole genome sequencing data, it becomes practical to mine STR profiles in silico from genome sequences. Software tools such as lobSTR and STR-FM have been developed to address these demands, which are, however, built upon whole genome reads mapping tools, and thus may not be sensitive enough.
resultsIn this paper, we present a standalone software tool STRScan that uses a greedy algorithm for targeted STR profiling in next-generation sequencing (NGS) data. STRScan was tested on the whole genome sequencing data from Venter genome sequencing and 1000 Genomes Project. The results showed that STRScan can profile 20% more STRs in the target set that are missed by lobSTR.
conclusionSTRScan is particularly useful for the NGS-based targeted STR profiling, e.g., in genetic and human identity testing. STRScan is available as open-source software at http://darwin.informatics.indiana.edu/str/ .
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