Reference-free transcriptome assembly for short and long reads

If you use RNA-Bloom in your research, please cite our manuscript(s).
Long-read RNA-seq assembly:
Ka Ming Nip, Saber Hafezqorani, Kristina K. Gagalova, Readman Chiu, Chen Yang, René L. Warren, and Inanc Birol. Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2. Nature Communications. 2023 May 22;14(1):2940. doi: 10.1038/s41467-023-38553-y

Short-read RNA-seq assembly
Ka Ming Nip, Readman Chiu, Chen Yang, Justin Chu, Hamid Mohamadi, René L. Warren, and Inanc Birol. RNA-Bloom enables reference-free and reference-guided sequence assembly for single-cell transcriptomes. Genome Research. 2020 Aug;30(8):1191-1200. doi: 10.1101/gr.260174.119. Epub 2020 Aug 17.

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GitHub release page for RNA-Bloom:

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