{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T06:04:39Z","timestamp":1790661879680,"version":"4.1.0"},"reference-count":15,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T00:00:00Z","timestamp":1790640000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Bioinform."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>Nanopore sequencing opens up new opportunities in transcriptome research due to the possibility of generating full-length isoform reads. However, currently available simulation software does not fully reproduce read truncation, a key feature of transcriptomic nanopore libraries.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>We developed TNRSim (Truncated Nanopore Reads Simulator), a nanopore transcriptome library simulator designed to reproduce realistic read-length distributions, sequencing errors, and quality scores. We further used simulated datasets with known isoform abundances to benchmark widely used isoform quantification tools.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>TNRSim reproduced characteristic read-truncation patterns observed in empirical direct RNA sequencing datasets and provided improvements in read-length distribution, mismatch, and quality-score simulation compared with existing approaches. In a closed-set benchmark of isoform quantification methods, oarfish achieved the highest quantification accuracy among the tested tools.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>TNRSim provides a framework for realistic simulation of transcriptomic nanopore sequencing data and enables controlled benchmarking of computational methods for isoform-level analysis.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fbinf.2026.1694068","type":"journal-article","created":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T05:50:44Z","timestamp":1790661044000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["TNRSim \u2014 a simulator of truncated oxford nanopore direct RNA long reads for isoform analysis"],"prefix":"10.3389","volume":"6","author":[{"given":"Anna","family":"Kozlova","sequence":"first","affiliation":[{"name":"Institute of Biomedical Chemistry","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Artemiy","family":"Sakharov","sequence":"additional","affiliation":[{"name":"Institute of Biomedical Chemistry","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Svetlana","family":"Tarbeeva","sequence":"additional","affiliation":[{"name":"Institute of Biomedical Chemistry","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ekaterina","family":"Ilgisonis","sequence":"additional","affiliation":[{"name":"Institute of Biomedical Chemistry","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena","family":"Ponomarenko","sequence":"additional","affiliation":[{"name":"Institute of Biomedical Chemistry","place":["Moscow, Russia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,9,29]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"giaa061","DOI":"10.1093\/gigascience\/giaa061","article-title":"Trans-NanoSim characterizes and simulates nanopore RNA-sequencing data","volume":"9","author":"Hafezqorani","year":"2020","journal-title":"GigaScience"},{"key":"B2","doi-asserted-by":"publisher","first-page":"182","DOI":"10.1186\/s13059-021-02399-8","article-title":"LIQA: long-read isoform quantification and analysis","volume":"22","author":"Hu","year":"2021","journal-title":"Genome Biol."},{"key":"B3","volume-title":"Oarfish: Enhanced Probabilistic Modeling Leads to Improved Accuracy in Long Read Transcriptome Quantification","author":"Jousheghani","year":"2024"},{"key":"B4","doi-asserted-by":"publisher","first-page":"7316","DOI":"10.1038\/s41467-024-51584-3","article-title":"Accurate long-read transcript discovery and quantification at single-cell, pseudo-bulk and bulk resolution with isosceles","volume":"15","author":"Kabza","year":"2024","journal-title":"Nat. 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