Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment.
| العنوان: | Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment. |
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| المؤلفون: | Kovaka S, Hook PW, Jenike KM, Shivakumar V, Morina LB, Razaghi R, Timp W, Schatz MC |
| المصدر: | BioRxiv : the preprint server for biology [bioRxiv] 2024 Mar 10. Date of Electronic Publication: 2024 Mar 10. |
| نوع المنشور: | Preprint |
| اللغة: | English |
| بيانات الدورية: | Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE |
| مستخلص: | Nanopore signal analysis enables detection of nucleotide modifications from native DNA and RNA sequencing, providing both accurate genetic/transcriptomic and epigenetic information without additional library preparation. Presently, only a limited set of modifications can be directly basecalled (e.g. 5-methylcytosine), while most others require exploratory methods that often begin with alignment of nanopore signal to a nucleotide reference. We present Uncalled4, a toolkit for nanopore signal alignment, analysis, and visualization. Uncalled4 features an efficient banded signal alignment algorithm, BAM signal alignment file format, statistics for comparing signal alignment methods, and a reproducible de novo training method for k-mer-based pore models, revealing potential errors in ONT's state-of-the-art DNA model. We apply Uncalled4 to RNA 6-methyladenine (m6A) detection in seven human cell lines, identifying 26% more modifications than Nanopolish using m6Anet, including in several genes where m6A has known implications in cancer. Uncalled4 is available open-source at github.com/skovaka/uncalled4. |
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| معلومات مُعتمدة: | OT2 OD002751 United States OD NIH HHS; R01 HG009190 United States HG NHGRI NIH HHS; R01 HG010538 United States HG NHGRI NIH HHS; U01 CA253481 United States CA NCI NIH HHS |
| تواريخ الأحداث: | Date Created: 20240318 Latest Revision: 20240327 |
| رمز التحديث: | 20240327 |
| مُعرف محوري في PubMed: | PMC10942365 |
| DOI: | 10.1101/2024.03.05.583511 |
| PMID: | 38496646 |
| قاعدة البيانات: | MEDLINE |
| DOI: | 10.1101/2024.03.05.583511 |
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