rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data
By Elena Bushmanova, Dmitry Antipov, Alla L. Lapidus, Andrey D. Prjibelski. bioRxiv, 2018
697 citations recorded by the source corpus.
Summary Possibility to generate large RNA-seq 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 model organisms with finished and 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. In this paper we describe a novel transcriptome assembler called rnaSPAdes, which is developed on top of SPAdes genome assembler and explores surprising 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-Seq datasets, and briefly highlight strong and weak points of different assemblers. Availability and implementation rnaSPAdes is implemented in C++ and Python and is freely available at cab.spbu.ru/software/rnaspades/.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/df147004ebeb7fbd1d69bcdf4796410b6168425b
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In Molecular Biology
- Dmitry Meleshko
- Anton I. Korobeynikov
- Jillian F. Banfield
- Alla L. Lapidus
- Dmitry Antipov
- Andrey D. Prjibelski
- Patrick S. G. Chain
- Chien-Chi Lo
Citations in the corpus
- Advances and Challenges in Metatranscriptomic Analysis (2019, background): “, 2013), and rnaSPAdes (Bushmanova et al., 2019) attempt to account for the issues in transcriptome sequencing, but were originally designed to assemble transcripts from a single organism.”
- Petabase-scale sequence alignment catalyses viral discovery (2020, methodology): “coronaSPAdes constructs an assembly graph from a RNA-sequencing dataset (transcriptome, meta-transcriptome, and meta-virome are supported), removing expected sequencing artifacts such as low-complexity (poly-A / poly-T) tips, edges, single-strand chimeric loops or doublestrand hairpins [52] and subs”
- Using SPAdes De Novo Assembler (2020, methodology): “However, rnaSPAdes implements different simplification algorithms, which were designed specifically for transcriptomic data (Bushmanova et al., 2019).”
- Sequence Analysis (2020, critical): “In contrast, a conventional de novo transcriptome assembler, rnaSPAdes (Bushmanova et al. 2019), failed to restore any isoforms with unique assignments for this particular gene.”