Show simple item record

dc.contributor.authorYu, Ting
dc.contributor.authorLiu, Juntao
dc.contributor.authorGao, Xin
dc.contributor.authorLi, Guojun
dc.date.accessioned2020-01-30T11:55:16Z
dc.date.available2020-01-30T11:55:16Z
dc.date.issued2020-01-27
dc.identifier.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
dc.identifier.doi10.1093/bioinformatics/btaa052
dc.identifier.urihttp://hdl.handle.net/10754/661333
dc.description.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.
dc.description.sponsorshipThis 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.
dc.publisherOxford University Press (OUP)
dc.relation.urlhttps://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa052/5716327
dc.rightsThis is a pre-copyedited, author-produced PDF of an article accepted for publication in Bioinformatics (Oxford, England) following peer review. The version of record is available online at: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa052/5716327.
dc.titleiPAC: A genome-guided assembler of isoforms via phasing and combing paths.
dc.typeArticle
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer Science Program
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.contributor.departmentStructural and Functional Bioinformatics Group
dc.identifier.journalBioinformatics (Oxford, England)
dc.rights.embargodate2021-01-28
dc.eprint.versionPost-print
dc.contributor.institutionSchool of Mathematics, Shandong University, Jinan, China.
kaust.personGao, Xin
kaust.grant.numberFCC/1/1976-18-01
kaust.grant.numberFCC/1/1976-23-01
kaust.grant.numberFCC/1/1976-25-01
kaust.grant.numberFCC/1/1976-26-01
refterms.dateFOA2020-01-30T12:29:22Z
dc.date.published-online2020-01-27
dc.date.published-print2020-05-01


Files in this item

Thumbnail
Name:
BIOINF-2019-1908.R1_Proof_hi.pdf
Size:
495.4Kb
Format:
PDF
Description:
Accepted manuscript

This item appears in the following Collection(s)

Show simple item record