Research output: Contribution to journal › Article › peer-review
Extending rnaSPAdes functionality for hybrid transcriptome assembly. / Prjibelski, Andrey D.; Puglia, Giuseppe D.; Antipov, Dmitry; Bushmanova, Elena; Giordano, Daniela; Mikheenko, Alla; Vitale, Domenico; Lapidus, Alla.
In: BMC Bioinformatics, Vol. 21, No. Suppl 12, 302, 24.07.2020, p. 302.Research output: Contribution to journal › Article › peer-review
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TY - JOUR
T1 - Extending rnaSPAdes functionality for hybrid transcriptome assembly
AU - Prjibelski, Andrey D.
AU - Puglia, Giuseppe D.
AU - Antipov, Dmitry
AU - Bushmanova, Elena
AU - Giordano, Daniela
AU - Mikheenko, Alla
AU - Vitale, Domenico
AU - Lapidus, Alla
N1 - Funding Information: Publication of this supplement is funded by Russian Science Foundation (grant number 19-14-00172).
PY - 2020/7/24
Y1 - 2020/7/24
N2 - Background: De novo RNA-Seq assembly is a powerful method for analysing transcriptomes when the reference genome is not available or poorly annotated. However, due to the short length of Illumina reads it is usually impossible to reconstruct complete sequences of complex genes and alternative isoforms. Recently emerged possibility to generate long RNA reads, such as PacBio and Oxford Nanopores, may dramatically improve the assembly quality, and thus the consecutive analysis. While reference-based tools for analysing long RNA reads were recently developed, there is no established pipeline for de novo assembly of such data. Results: In this work we present a novel method that allows to perform high-quality de novo transcriptome assemblies by combining accuracy and reliability of short reads with exon structure information carried out from long error-prone reads. The algorithm is designed by incorporating existing hybridSPAdes approach into rnaSPAdes pipeline and adapting it for transcriptomic data. Conclusion: To evaluate the benefit of using long RNA reads we selected several datasets containing both Illumina and Iso-seq or Oxford Nanopore Technologies (ONT) reads. Using an existing quality assessment software, we show that hybrid assemblies performed with rnaSPAdes contain more full-length genes and alternative isoforms comparing to the case when only short-read data is used.
AB - Background: De novo RNA-Seq assembly is a powerful method for analysing transcriptomes when the reference genome is not available or poorly annotated. However, due to the short length of Illumina reads it is usually impossible to reconstruct complete sequences of complex genes and alternative isoforms. Recently emerged possibility to generate long RNA reads, such as PacBio and Oxford Nanopores, may dramatically improve the assembly quality, and thus the consecutive analysis. While reference-based tools for analysing long RNA reads were recently developed, there is no established pipeline for de novo assembly of such data. Results: In this work we present a novel method that allows to perform high-quality de novo transcriptome assemblies by combining accuracy and reliability of short reads with exon structure information carried out from long error-prone reads. The algorithm is designed by incorporating existing hybridSPAdes approach into rnaSPAdes pipeline and adapting it for transcriptomic data. Conclusion: To evaluate the benefit of using long RNA reads we selected several datasets containing both Illumina and Iso-seq or Oxford Nanopore Technologies (ONT) reads. Using an existing quality assessment software, we show that hybrid assemblies performed with rnaSPAdes contain more full-length genes and alternative isoforms comparing to the case when only short-read data is used.
KW - transcriptomics
KW - transcriptome assembly
KW - RNA-Seq
KW - Oxford nanopores
KW - Iso-seq
KW - Hybrid assembly
KW - De novo assembly
KW - Algorithms
KW - Databases, Genetic
KW - Humans
KW - MCF-7 Cells
KW - Nanopores
KW - RNA-Seq
KW - Reproducibility of Results
KW - Transcriptome/genetics
KW - Iso-seq
KW - De novo assembly
KW - Oxford nanopores
KW - QUALITY ASSESSMENT
KW - Transcriptome assembly
KW - Transcriptomics
KW - Hybrid assembly
UR - http://www.scopus.com/inward/record.url?scp=85088528928&partnerID=8YFLogxK
UR - https://www.mendeley.com/catalogue/43b7f243-03f1-3579-bc16-92a5d5c3ec91/
U2 - 10.1186/s12859-020-03614-2
DO - 10.1186/s12859-020-03614-2
M3 - Article
C2 - 32703149
AN - SCOPUS:85088528928
VL - 21
SP - 302
JO - BMC Bioinformatics
JF - BMC Bioinformatics
SN - 1471-2105
IS - Suppl 12
M1 - 302
ER -
ID: 61160726