Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2
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 l...
| Main Authors: | , , , , , , |
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| Format: | Journal Article |
| Language: | English |
| Published: |
2023
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| Subjects: | |
| Online Access: | http://hdl.handle.net/20.500.11937/96867 |
| _version_ | 1848766201449152512 |
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| author | Nip, K.M. Hafezqorani, S. Gagalova, Kristina Chiu, R. Yang, C. Warren, R.L. Birol, I. |
| author_facet | Nip, K.M. Hafezqorani, S. Gagalova, Kristina Chiu, R. Yang, C. Warren, R.L. Birol, I. |
| author_sort | Nip, K.M. |
| building | Curtin Institutional Repository |
| collection | Online Access |
| description | 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. |
| first_indexed | 2025-11-14T11:47:23Z |
| format | Journal Article |
| id | curtin-20.500.11937-96867 |
| institution | Curtin University Malaysia |
| institution_category | Local University |
| language | eng |
| last_indexed | 2025-11-14T11:47:23Z |
| publishDate | 2023 |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | curtin-20.500.11937-968672025-02-13T00:58:13Z Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2 Nip, K.M. Hafezqorani, S. Gagalova, Kristina Chiu, R. Yang, C. Warren, R.L. Birol, I. Transcriptome RNA High-Throughput Nucleotide Sequencing Gene Expression Profiling Sequence Analysis, RNA RNA Gene Expression Profiling Sequence Analysis, RNA High-Throughput Nucleotide Sequencing Transcriptome 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. 2023 Journal Article http://hdl.handle.net/20.500.11937/96867 10.1038/s41467-023-38553-y eng http://creativecommons.org/licenses/by/4.0/ fulltext |
| spellingShingle | Transcriptome RNA High-Throughput Nucleotide Sequencing Gene Expression Profiling Sequence Analysis, RNA RNA Gene Expression Profiling Sequence Analysis, RNA High-Throughput Nucleotide Sequencing Transcriptome Nip, K.M. Hafezqorani, S. Gagalova, Kristina Chiu, R. Yang, C. Warren, R.L. Birol, I. Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2 |
| title | Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2 |
| title_full | Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2 |
| title_fullStr | Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2 |
| title_full_unstemmed | Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2 |
| title_short | Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2 |
| title_sort | reference-free assembly of long-read transcriptome sequencing data with rna-bloom2 |
| topic | Transcriptome RNA High-Throughput Nucleotide Sequencing Gene Expression Profiling Sequence Analysis, RNA RNA Gene Expression Profiling Sequence Analysis, RNA High-Throughput Nucleotide Sequencing Transcriptome |
| url | http://hdl.handle.net/20.500.11937/96867 |