NanoMnT: an STR analysis tool for Oxford Nanopore sequencing data driven by a comprehensive analysis of error profile in STR regions

GigaScience, Journal Year: 2025, Volume and Issue: 14

Published: Jan. 1, 2025

Abstract Oxford Nanopore Technology (ONT) sequencing is a third-generation technology that enables cost-effective long-read sequencing, with broad applications in biological research. However, its high error rate low-complexity regions hampers short tandem repeat (STR)–related To address this, we generated comprehensive STR profile of ONT by analyzing publicly available datasets. We show the influenced not only length but also unit and flanking sequences regions. Interestingly, certain were associated higher accuracy, suggesting loci are more suitable for compared to other loci. While base quality scores substitution errors within lower than those correctly sequenced bases, such patterns observed indel errors. Furthermore, choosing most recent basecaller version using super accuracy model significantly improved accuracy. Finally, present NanoMnT, lightweight Python tool corrects data estimates allele sizes. NanoMnT leverages characteristics when estimating size exhibits superior results 1-bp- 2-bp existing tools. By integrating our findings, estimation Ax10 repeats from 55% 78% up 85% excluding unfavorable sequences. Using utility findings identifying microsatellite instability status cancer data. at https://github.com/18parkky/NanoMnT.

Language: Английский

Retroelement co-option disrupts the cancer transcriptional programme

Genome Medicine, Journal Year: 2025, Volume and Issue: 17(1)

Published: May 7, 2025

Language: Английский