iPAC: A genome-guided assembler of isoforms via phasing and combing paths.
Name:
BIOINF-2019-1908.R1_Proof_hi.pdf
Size:
495.4Kb
Format:
PDF
Description:
Accepted manuscript
Type
ArticleKAUST Department
Computational Bioscience Research Center (CBRC)Computer Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Structural and Functional Bioinformatics Group
KAUST Grant Number
FCC/1/1976-18-01FCC/1/1976-23-01
FCC/1/1976-25-01
FCC/1/1976-26-01
Date
2020-01-27Online Publication Date
2020-01-27Print Publication Date
2020-05-01Embargo End Date
2021-01-28Permanent link to this record
http://hdl.handle.net/10754/661333
Metadata
Show full item recordAbstract
MOTIVATION:Full-length transcript reconstruction is very important and quite challenging for the widely used RNA-seq data analysis. Currently available RNA-seq assemblers generally suffered from serious limitations in practical applications, such as low assembly accuracy and incompatibility with latest alignment tools. RESULTS:We introduce iPAC, a new genome-guided assembler for reconstruction of isoforms, which revolutionizes the usage of paired-end and sequencing depth information via phasing and combing paths over a newly designed phasing graph. Tested on both simulated and real datasets, it is to some extent superior to all the salient assemblers of the same kind. Especially, iPAC is significantly powerful in recovery of lowly expressed transcripts while others are not. AVAILABILITY: iPAC is freely available at http://sourceforge.net/projects/transassembly/files. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.Citation
Yu, T., Liu, J., Gao, X., & Li, G. (2020). iPAC: A genome-guided assembler of isoforms via phasing and combing paths. Bioinformatics. doi:10.1093/bioinformatics/btaa052Sponsors
This work was supported by the National Natural Science Foundation of China with codes 11931008, 61801265, 61877064, 31571354 and 61771009, and the Natural Science Foundation of Shandong Province with code ZR2018PA001, and by funding from King Abdullah University of Science and Technology (KAUST), under award number FCC/1/1976-18-01, FCC/1/1976-23-01, FCC/1/1976-25-01, FCC/1/1976-26-01, FCS/1/4102-02-01, and URF/1/4098-01-01. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Publisher
Oxford University Press (OUP)Journal
BioinformaticsAdditional Links
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa052/5716327ae974a485f413a2113503eed53cd6c53
10.1093/bioinformatics/btaa052