{"doi":"10.1101/2022.08.07.503110","title":"Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2","abstract":"ABSTRACT Long-read sequencing technologies have improved significantly since their emergence. Their read lengths, potentially spanning entire transcripts, is advantageous for reconstructing transcriptomes. Existing long-read transcriptome assembly methods are primarily reference-based and to date, there is little focus on reference-free transcriptome assembly. We introduce RNA-Bloom2, a reference-free assembly method for long-read transcriptome sequencing data. Using simulated datasets and spike-in control data, we show that the transcriptome assembly quality of RNA-Bloom2 is competitive to those of reference-based methods. Furthermore, RNA-Bloom2 requires 27.0 to 80.6% of the peak memory and 3.6 to 10.8% of the total wall-clock runtime of a competing reference-free method. Finally, we showcase RNA-Bloom2 in assembling a transcriptome sample of Picea sitchensis (Sitka spruce). Since our method does not rely on a reference, it sets up the groundwork for large-scale comparative transcriptomics where high-quality draft genome assemblies are not readily available.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2022,"id":298019,"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":7,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9489,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2022-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":473705,"name":"Saber Hafezqorani","orcid":"0000-0003-0553-9227","position":1,"is_corresponding":false},{"id":802698,"name":"Kristina Gagalova","orcid":"0000-0002-5975-0805","position":2,"is_corresponding":false},{"id":22085,"name":"Readman Chiu","orcid":"0000-0002-2215-5535","position":3,"is_corresponding":false},{"id":473706,"name":"Chen Yang","orcid":"0000-0002-5144-7748","position":4,"is_corresponding":false},{"id":18717,"name":"René L. Warren","orcid":"0000-0002-9890-2293","position":5,"is_corresponding":false},{"id":18731,"name":"Inanc Birol","orcid":"0000-0003-0950-7839","position":6,"is_corresponding":false},{"id":473708,"name":"Ka Ming Nip","orcid":"0000-0002-1574-3363","position":0,"is_corresponding":true}],"reference_count":42,"raw_metadata":null,"created_at":"2026-07-19T00:31:31.270564Z","pmid":null,"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":[]}