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bioRxiv · 10.1101/2022.08.07.503110

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

Nip, K. M.·Hafezqorani, S.·Gagalova, K. K.·Chiu, R.·Yang, C.·Warren, R. L.·Birol, I.
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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.

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Nip, K. M., Hafezqorani, S., Gagalova, K. K., Chiu, R., Yang, C., Warren, R. L., Birol, I.. 2022-08-07. Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2. https://doi.org/10.1101/2022.08.07.503110

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