Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2
Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2
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.
Nip Ka Ming、Gagalova Kristina K.、Chiu Readman、Warren Ren¨| L.、Yang Chen、Birol Inanc、Hafezqorani Saber
Canada?ˉs Michael Smith Genome Sciences Centre||Bioinformatics Graduate Program, University of British ColumbiaCanada?ˉs Michael Smith Genome Sciences Centre||Bioinformatics Graduate Program, University of British ColumbiaCanada?ˉs Michael Smith Genome Sciences CentreCanada?ˉs Michael Smith Genome Sciences CentreCanada?ˉs Michael Smith Genome Sciences Centre||Bioinformatics Graduate Program, University of British ColumbiaCanada?ˉs Michael Smith Genome Sciences Centre||Department of Medical Genetics, University of British ColumbiaCanada?ˉs Michael Smith Genome Sciences Centre||Bioinformatics Graduate Program, University of British Columbia
生物科学研究方法、生物科学研究技术分子生物学生物工程学
RNA sequencingLong readsTranscriptome assemblyTranscript isoformsNanopore sequencingAlgorithm
Nip Ka Ming,Gagalova Kristina K.,Chiu Readman,Warren Ren¨| L.,Yang Chen,Birol Inanc,Hafezqorani Saber.Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2[EB/OL].(2025-03-28)[2025-06-04].https://www.biorxiv.org/content/10.1101/2022.08.07.503110.点此复制
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