{"doi":"10.1101/2023.08.23.554392","title":"SQANTI-SIM: a simulator of controlled transcript novelty for lrRNA-seq benchmark","abstract":"Long-read RNA-seq has emerged as a powerful tool for transcript discovery, even in well-annotated organisms. However, assessing the accuracy of different methods in identifying annotated and novel transcripts remains a challenge. Here, we present SQANTI-SIM, a versatile utility that wraps around popular long-read simulators to allow precise management of transcript novelty based on the structural categories defined by SQANTI3. By selectively excluding specific transcripts from the reference dataset, SQANTI-SIM effectively emulates scenarios involving unannotated transcripts. Furthermore, the tool provides customizable features and supports the simulation of additional types of data, representing the first multi-omics simulation tool for the lrRNA-seq field. We demonstrate the effectiveness of SQANTI-SIM by benchmarking five transcriptome reconstruction pipelines using the simulated data.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2023,"id":397127,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":2,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9484,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":849863,"name":"Tianyuan Liu","orcid":"0000-0002-8561-6239","position":1,"is_corresponding":false},{"id":989497,"name":"Francisco J. Pardo-Palacios","orcid":"0000-0002-3067-0166","position":2,"is_corresponding":false},{"id":20402,"name":"Ana Conesa","orcid":"0000-0001-9597-311X","position":3,"is_corresponding":false},{"id":1160009,"name":"Jorge Mestre‐Tomás","orcid":"0000-0002-8983-3417","position":0,"is_corresponding":true}],"reference_count":44,"raw_metadata":null,"created_at":"2026-07-19T01:19:35.497854Z","pmid":"37662216","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}