Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2

作者：Ka Ming Nip, Saber Hafezqorani, Kristina Gagalova, Readman Chiu, Chen Yang, René L. Warren, İnanç Birol · 发表于：Nature Communications · 年份：2023 · DOI：10.1038/s41467-023-38553-y · 被引用次数：51 · 研究领域：Genomics and Phylogenetic Studies、RNA and protein synthesis mechanisms、RNA modifications and cancer

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 [ https://github.com/bcgsc/RNA-Bloom ]", 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, we find that 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 further sets the groundwork for large-scale comparative transcriptomics where high-quality draft genome assemblies are not readily available.