iPAC: A genome-guided assembler of isoforms via phasing and combing paths.
KAUST DepartmentComputational Bioscience Research Center (CBRC)
Computer Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Structural and Functional Bioinformatics Group
Online Publication Date2020-01-27
Print Publication Date2020-05-01
Embargo End Date2021-01-28
Permanent link to this recordhttp://hdl.handle.net/10754/661333
MetadataShow full item record
AbstractMOTIVATION: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.
CitationYu, 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/btaa052
SponsorsThis 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.
PublisherOxford University Press (OUP)
JournalBioinformatics (Oxford, England)