Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2.
Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2.
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DOI：
10.1038/s41467-023-38553-y
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发表时间：
2023-05-22
影响因子：
16.6
通讯作者：
Birol, Inanc
中科院分区：
文献类型：
--
作者：
Nip, Ka Ming;Hafezqorani, Saber;Gagalova, Kristina K.;Chiu, Readman;Yang, Chen;Warren, Rene L.;Birol, Inanc
长读段测序技术自出现以来已经有了显著的改进。它们的阅读长度，可能跨越整个转录本，有利于重建转录组。现有的长读段转录组组装方法主要是基于参考的，并且迄今为止，很少关注无参考转录组组装。我们介绍“RNA-Bloom 2 [https：//github.com/bcgsc/RNA-Bloom]”，这是一种用于长读转录组测序数据的无参考组装方法。使用模拟数据集和加标对照数据，我们表明RNA-Bloom 2的转录组组装质量与基于参考的方法相比具有竞争力。此外，我们发现RNA-Bloom 2需要27.0%至80.6%的峰值内存和3.6%至10.8%的总挂钟运行时间的竞争性无参考方法。最后，我们展示了RNA-Bloom 2在组装云杉（锡特卡云杉）的转录组样本。由于我们的方法不依赖于参考，它进一步为大规模比较转录组学奠定了基础，其中高质量的基因组草图组装并不容易获得。大多数现有的长阅读转录组组装方法依赖于参考基因组和转录本注释，而无参考方法仍然很少。在这里，Nip等人介绍了RNA-Bloom 2，一种无需引用的方法，它比其他无需引用的方法需要更少的内存和运行时间。
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. Most existing long-read transcriptome assembly methods rely on reference genomes and transcript annotations, while reference-free methods remain scarce. Here, Nip et al. introduce RNA-Bloom2, a reference-free method that requires substantially less memory and runtime than other reference-free methods.
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