{"doi":"10.1101/2025.03.31.646392","title":"A little longer, a lot better: simulation-guided exploration of extended-length single-end barcoded reads for structural variant detection","abstract":"Accurate detection of genetic variants, including single nucleotide polymorphisms (SNPs), small insertions and deletions (INDELs), and structural variants (SVs), is essential for comprehensive genomic analysis. While short-read sequencing performs well for SNP and INDEL detection, it remains limited in resolving SVs, particularly in complex genomic regions, due to its short read length. Linked-read sequencing technologies, such as single-tube Long Fragment Read (stLFR), partially address this limitation by incorporating molecular barcodes to provide long-range information. In this study, we evaluate conventional paired-end linked reads (PE100_stLFR) and explore a conceptual extension: long single-end barcoded reads of 500 bp (SE500_stLFR) and 1000 bp (SE1000_stLFR). We developed stLFR-sim, a Python-based simulator that reproduces the stLFR workflow and enables realistic benchmarking. Using a high-quality T2T assembly of HG002, we generated multiple datasets across 12 sequencing configurations. SVs were called using Aquila_stLFR (v2) and benchmarked against the Genome in a Bottle (GIAB) HG002 SV truth set with Truvari. We show that simulated PE100_stLFR closely matches real data, validating the simulation framework. Increasing read length consistently improves SV detection accuracy, with SE1000_stLFR achieving the best performance and approaching long-read methods while outperforming short-read and pangenome-based approaches. Collectively, our results highlight the strong potential of long single-end barcoded reads for improving SV detection, and suggest that even modest increases in read length, when combined with barcode information, can provide a cost-effective and practical strategy for enhancing future sequencing technologies and SV discovery.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2025,"id":563871,"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":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9481,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2025-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1466761,"name":"Yichen Henry Liu","orcid":"0009-0009-7817-1081","position":1,"is_corresponding":false},{"id":1336488,"name":"Han Liu","orcid":"0009-0009-1447-960X","position":2,"is_corresponding":false},{"id":51373,"name":"Zhenmiao Zhang","orcid":"0000-0003-3748-1664","position":3,"is_corresponding":false},{"id":522501,"name":"Lu Zhang","orcid":"0000-0002-2794-7371","position":4,"is_corresponding":false},{"id":1445586,"name":"Brock A. Peters","orcid":"0000-0002-5137-3902","position":5,"is_corresponding":false},{"id":280981,"name":"Xin Zhou","orcid":"0000-0003-4015-4787","position":6,"is_corresponding":false},{"id":998158,"name":"Can Luo","orcid":"0000-0002-7311-5963","position":0,"is_corresponding":true}],"reference_count":19,"raw_metadata":null,"created_at":"2026-07-19T02:56:17.117043Z","pmid":"42039607","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":[]}