rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data
The possibility of generating large RNA-sequencing datasets has led to development of various reference-based and de novo transcriptome assemblers with their own strengths and limitations. While reference-based tools are widely used in various transcriptomic studies, their application is limited to...
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Published in | Gigascience Vol. 8; no. 9 |
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Main Authors | , , , |
Format | Journal Article |
Language | English |
Published |
United States
Oxford University Press
01.09.2019
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Online Access | Get full text |
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Abstract | The possibility of generating large RNA-sequencing datasets has led to development of various reference-based and de novo transcriptome assemblers with their own strengths and limitations. While reference-based tools are widely used in various transcriptomic studies, their application is limited to the organisms with finished and well-annotated genomes. De novo transcriptome reconstruction from short reads remains an open challenging problem, which is complicated by the varying expression levels across different genes, alternative splicing, and paralogous genes.
Herein we describe the novel transcriptome assembler rnaSPAdes, which has been developed on top of the SPAdes genome assembler and explores computational parallels between assembly of transcriptomes and single-cell genomes. We also present quality assessment reports for rnaSPAdes assemblies, compare it with modern transcriptome assembly tools using several evaluation approaches on various RNA-sequencing datasets, and briefly highlight strong and weak points of different assemblers.
Based on the performed comparison between different assembly methods, we infer that it is not possible to detect the absolute leader according to all quality metrics and all used datasets. However, rnaSPAdes typically outperforms other assemblers by such important property as the number of assembled genes and isoforms, and at the same time has higher accuracy statistics on average comparing to the closest competitors. |
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AbstractList | Background The possibility of generating large RNA-sequencing datasets has led to development of various reference-based and de novo transcriptome assemblers with their own strengths and limitations. While reference-based tools are widely used in various transcriptomic studies, their application is limited to the organisms with finished and well-annotated genomes. De novo transcriptome reconstruction from short reads remains an open challenging problem, which is complicated by the varying expression levels across different genes, alternative splicing, and paralogous genes. Results Herein we describe the novel transcriptome assembler rnaSPAdes, which has been developed on top of the SPAdes genome assembler and explores computational parallels between assembly of transcriptomes and single-cell genomes. We also present quality assessment reports for rnaSPAdes assemblies, compare it with modern transcriptome assembly tools using several evaluation approaches on various RNA-sequencing datasets, and briefly highlight strong and weak points of different assemblers. Conclusions Based on the performed comparison between different assembly methods, we infer that it is not possible to detect the absolute leader according to all quality metrics and all used datasets. However, rnaSPAdes typically outperforms other assemblers by such important property as the number of assembled genes and isoforms, and at the same time has higher accuracy statistics on average comparing to the closest competitors. BACKGROUNDThe possibility of generating large RNA-sequencing datasets has led to development of various reference-based and de novo transcriptome assemblers with their own strengths and limitations. While reference-based tools are widely used in various transcriptomic studies, their application is limited to the organisms with finished and well-annotated genomes. De novo transcriptome reconstruction from short reads remains an open challenging problem, which is complicated by the varying expression levels across different genes, alternative splicing, and paralogous genes. RESULTSHerein we describe the novel transcriptome assembler rnaSPAdes, which has been developed on top of the SPAdes genome assembler and explores computational parallels between assembly of transcriptomes and single-cell genomes. We also present quality assessment reports for rnaSPAdes assemblies, compare it with modern transcriptome assembly tools using several evaluation approaches on various RNA-sequencing datasets, and briefly highlight strong and weak points of different assemblers. CONCLUSIONSBased on the performed comparison between different assembly methods, we infer that it is not possible to detect the absolute leader according to all quality metrics and all used datasets. However, rnaSPAdes typically outperforms other assemblers by such important property as the number of assembled genes and isoforms, and at the same time has higher accuracy statistics on average comparing to the closest competitors. The possibility of generating large RNA-sequencing datasets has led to development of various reference-based and de novo transcriptome assemblers with their own strengths and limitations. While reference-based tools are widely used in various transcriptomic studies, their application is limited to the organisms with finished and well-annotated genomes. De novo transcriptome reconstruction from short reads remains an open challenging problem, which is complicated by the varying expression levels across different genes, alternative splicing, and paralogous genes. Herein we describe the novel transcriptome assembler rnaSPAdes, which has been developed on top of the SPAdes genome assembler and explores computational parallels between assembly of transcriptomes and single-cell genomes. We also present quality assessment reports for rnaSPAdes assemblies, compare it with modern transcriptome assembly tools using several evaluation approaches on various RNA-sequencing datasets, and briefly highlight strong and weak points of different assemblers. Based on the performed comparison between different assembly methods, we infer that it is not possible to detect the absolute leader according to all quality metrics and all used datasets. However, rnaSPAdes typically outperforms other assemblers by such important property as the number of assembled genes and isoforms, and at the same time has higher accuracy statistics on average comparing to the closest competitors. |
Author | Antipov, Dmitry Bushmanova, Elena Prjibelski, Andrey D Lapidus, Alla |
AuthorAffiliation | Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, 199004, 6 linia V.O. 11d, Russia |
AuthorAffiliation_xml | – name: Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, 199004, 6 linia V.O. 11d, Russia |
Author_xml | – sequence: 1 givenname: Elena surname: Bushmanova fullname: Bushmanova, Elena organization: Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, 199004, 6 linia V.O. 11d, Russia – sequence: 2 givenname: Dmitry surname: Antipov fullname: Antipov, Dmitry organization: Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, 199004, 6 linia V.O. 11d, Russia – sequence: 3 givenname: Alla surname: Lapidus fullname: Lapidus, Alla organization: Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, 199004, 6 linia V.O. 11d, Russia – sequence: 4 givenname: Andrey D surname: Prjibelski fullname: Prjibelski, Andrey D organization: Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, 199004, 6 linia V.O. 11d, Russia |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/31494669$$D View this record in MEDLINE/PubMed |
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