About: BOAssembler: A Bayesian Optimization Framework to Improve RNA-Seq Assembly Performance

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An Entity of Type : schema:ScholarlyArticle, within Data Space : wasabi.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	BOAssembler: A Bayesian Optimization Framework to Improve RNA-Seq Assembly Performance
Creator	Jiang, Yihan Kannan, Sreeram Mao, Shunfu Mathew, Edwin
Source	PMC
abstract	High throughput sequencing of RNA (RNA-Seq) can provide us with millions of short fragments of RNA transcripts from a sample. How to better recover the original RNA transcripts from those fragments (RNA-Seq assembly) is still a difficult task. For example, RNA-Seq assembly tools typically require hyper-parameter tuning to achieve good performance for particular datasets. This kind of tuning is usually unintuitive and time-consuming. Consequently, users often resort to default parameters, which do not guarantee consistent good performance for various datasets. Results: Here we propose BOAssembler, a framework that enables end-to-end automatic tuning of RNA-Seq assemblers, based on Bayesian Optimization principles. Experiments show this data-driven approach is effective to improve the overall assembly performance. The approach would be helpful for downstream (e.g. gene, protein, cell) analysis, and more broadly, for future bioinformatics benchmark studies. Availability: https://github.com/shunfumao/boassembler.
has issue date	2020-02-01(xsd:dateTime)
bibo:doi	10.1007/978-3-030-42266-0_15
has license	no-cc
sha1sum (hex)	87ba625767179c70a86cb012d88ef62d1c9f25df
schema:url	https://doi.org/10.1007/978-3-030-42266-0_15
resource representing a document's title	BOAssembler: A Bayesian Optimization Framework to Improve RNA-Seq Assembly Performance
has PubMed Central identifier	PMC7197064
schema:publication	Algorithms for Computational Biology
resource representing a document's body	covid:87ba625767179c70a86cb012d88ef62d1c9f25df#body_text
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