Next-generation sequencing-based tools or nanopore-based tools: Which is more suitable for short tandem repeats genotyping of nanopore sequencing?
Open accessAbstract
Motivation: Short tandem repeats (STRs) are widely recognized as critical genetic markers for individual identification. Nanopore sequencing technology holds promise as an effective tool for onsite STR detection owing to its portability. Initially, low sequencing quality led to the development of various genotyping tools specifically tailored for nanopore data. However, recent advancements in nanopore sequencing quality suggest that tools designed for next-generation sequencing (NGS) may be more suitable for analyzing nanopore data than those specifically developed for nanopore sequencing. Results: We selected two sequencing platforms, MinION Mk1C, and PolySeqOne, to generate sequencing data from 61 unrelated individual samples. Samples were amplified using a custom NanoSTR panel that included 31 autosomal STRs (A-STRs) and 31 Y chromosomal STRs (Y-STRs). Sequencing data were analyzed using four distinct tools: NASTRA, STRspy, STRinNGS, and STRait Razor. Our findings indicated that STRinNGS showed greater accuracy for both A-STRs and Y-STRs, enabling the accurate detection of a broad range of STRs. Compared with STRinNGS, NASTRA exhibited greater STR depth and featured more non-integer stutters. Therefore, in practical applications, STRinNGS demonstrates high reliability in genotyping. Availability and implementation: NASTRA, STRspy, STRinNGS and STRait Razor, which can be accessed via the following links: https://github.com/renzilin/NASTRA, https://github.com/unique379r/strspy, https://bitbucket.org/rirgabiss/strinngs/src/master, and https://github.com/Ahhgust/STRaitRazor, respectively. The commands during process are provided as requested by the corresponding author.
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Expert review remains crucial for STR profile interpretation despite software solutions.
“While software solutions like GeneMapper® ID-X [41], STRait Razor [42], and the open-source Haplotype inference and phasing for STRs (HipSTR) [43] include peak-height ratios, heterozygosity thresholds, and ladder alignment checks to minimize false calls, expert review remains crucial [44].”
From Genetic Insights into the Economic Toll of Cell Line Misidentification: A Comprehensive Review (2026) · cites this paper as [44]
The Results (§3.3 and §3.5; page unavailable) document STR genotyping errors and limitations of software tools. The Conclusion (§4; page unavailable) calls for future algorithm optimization, but neither it nor the passages retrieved for manual or expert review says that expert review of STR profiles remains crucial. (LLM, conf=0.76)
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Cited by
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Genetic Insights into the Economic Toll of Cell Line Misidentification: A Comprehensive Review
Weiskirchen, R. (2026) · Medical Sciences · doi:10.3390/medsci14010025 · Cited by 4 · see citing works
- Authors
- Han, W., Zhang, X., Zhang, Q., & Zhou, Z.
- Affiliations
- Bioinformatics Center of AMMS , Beijing 100850,
- Chinese Academy of Sciences (CN)
- Corresponding author
- Zhang, Qingzhen
- Zhou, Zhe
- Venue
- Bioinformatics Advances
- Publisher
- Oxford University Press (OUP)
- Published
- 2024-12-26
- Volume
- 5
- Issue
- 1
- Pages
- vbaf119-vbaf119
- ISSN
- 2635-0041 (ISSN-L)
- PMC
- PMC12167636
- OpenAlex
- W4411318424
- Cited by
- 3
- References
- 0
- Citations by year
- 2026: 3
- FWCI
- 0.80
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Bioinformatics Advances (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- microsatellite markers, STR genotyping, nanopore sequencing, autosomal STRs, Y-chromosome short tandem repeats, individual identification, genotyping accuracy
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