ArticleBioinformatics (Oxford, England)2023
WarpSTR: determining tandem repeat lengths using raw nanopore signals.
Article in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
9 citing papers in PubMed.
- Somatic mosaicism in the brain: linking development, ageing and neurodegeneration.Nature reviews. Neurology · 2026Review
- SquiDBase: a community resource of raw nanopore data from microbes.NAR genomics and bioinformatics · 2026Article
- Computational tools for tandem repeat detection using long-read sequencing.Briefings in bioinformatics · 2026Review
- Enhanced detection and genotyping of disease-associated tandem repeats using HMMSTR and targeted long-read sequencing.Nucleic acids research · 2025Article
- Navigating triplet repeats sequencing: concepts, methodological challenges and perspective for Huntington's disease.Nucleic acids research · 2025Review
- NanoMnT: an STR analysis tool for Oxford Nanopore sequencing data driven by a comprehensive analysis of error profile in STR regions.GigaScience · 2025Article
- Get ready for short tandem repeats analysis using long reads-the challenges and the state of the art.Frontiers in genetics · 2025Review
- Nanopore DNA sequencing technologies and their applications towards single-molecule proteomics.Nature chemistry · 2024Review
- A comparison of Oxford nanopore library strategies for bacterial genomics.BMC genomics · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationShort 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.
resultsHere, 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. AVAILABILITY AND IMPLEMENTATION: WarpSTR is freely available at https://github.com/fmfi-compbio/warpstr.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.