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Coral accurately bridges paired-end reads alignment
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Citation:
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Originator:The Pennsylvania State University
Publication_Date:2020
Title:
Coral accurately bridges paired-end reads alignment
Other_Citation_Details:
Qian Shi and Mingfu Shao (The Pennsylvania State University-University Park)
Online_Linkage: http://www.datacommons.psu.edu/
Description:
Abstract: 
Motivation: The established high-throughput RNA-seq technologies usually produce paired-end reads. A challenging problem is therefore to computationally infer the alignment of entire fragments given the alignment of the two mate ends. Solving this problem essentially provide longer RNA-seq reads, and hence benefits downstream RNA-seq analysis.
Results: We introduce Coral, a new tool that can accurately bridge paired-end RNA-seq reads. The core of Coral is a novel optimization formulation that can capture the most reliable bridging path while also filter out false paths. An efficient dynamic programming algorithm is designed to calculate the top N optimum. Coral implements a consensus approach to select the best solution among the N candidates by taking into account the distribution of fragment length. Coral is modular, can be easily incorporated into existing RNA-seq analysis pipeline. We show that Coral can improve transcript assembly by a large margin: on average over 2377 RNA-seq samples from GTEx, the improvement (measured with adjusted precision) is 7.5% and 11.2% when Coral is incorporated with StringTie and Scallop, respectively.
Availability: Coral is open-source, freely available at GitHub (https://github.com/Shao-Group/coral) and Bioconda. Scripts, datasets and documentations that can reproduce all experimental results in this paper are available at https://github.com/Shao-Group/coraltest.
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Calendar_Date:2020
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The University excludes any and all implied warranties, including warranties or merchantability and fitness for a particular purpose.
The University makes no warranty or representation, either express or implied, with respect to the FILES or accompanying documentation, including its quality, performance, merchantability, or fitness for a particular purpose. The FILES and documentation are provided "as is" and the USER assumes the entire risk as to its quality and performance.
The University will not be liable for any direct, indirect, special, incidental, or consequential damages arising out of the use or inability to use the FILES or any accompanying documentation.
The USER is granted permission to translate and add value to the FILES for the use of the FILES on its computer hardware; provided, however, that the USER annually notify the University of any customizing or value-adding work done.
Point_of_Contact:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization:Penn State
Contact_Person:Mingfu Shao
Contact_Position:College of Engineering
Contact_Address:
Address_Type:mailing address
City:University Park
State_or_Province:Pennsylvania
Postal_Code:16802
Country:USA
Contact_Voice_Telephone:mxs2589@psu.edu
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Contact_Information:
Contact_Person_Primary:
Contact_Organization:Penn State Data Commons
Contact_Address:
Address_Type:mailing and physical address
Address: 
115 Land and Water Building
City:University Park
State_or_Province:Pennsylvania
Postal_Code:16802
Country:United States
Contact_Voice_Telephone:(814) 865 - 8792
Contact_Electronic_Mail_Address:datacommons@psu.edu
Distribution_Liability: 
The USER shall indemnify, save harmless, and, if requested, defend those parties involved with the development and distribution of this data, their officers, agents, and employees from and against any suits, claims, or actions for injury, death, or property damage arising out of the use of or any defect in the FILES or any accompanying documentation. Those parties involved with the development and distribution excluded any and all implied warranties, including warranties or merchantability and fitness for a particular purpose and makes no warranty or representation, either express or implied, with respect to the FILES or accompanying documentation, including its quality, performance, merchantability, or fitness for a particular purpose. The FILES and documentation are provided "as is" and the USER assumes the entire risk as to its quality and performance. Those parties involved with the development and distribution of this data will not be liable for any direct, indirect, special, incidental, or consequential damages arising out of the use or inability to use the FILES or any accompanying documentation.
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Contact_Information:
Contact_Organization_Primary:
Contact_Organization:Penn State Data Commons
Contact_Position:Metadata Coordinator
Contact_Address:
Address_Type:mailing address
Address: 
115 Land and Water Building
City:University Park
State_or_Province:Pennsylvania
Postal_Code:16802
Country:United States
Contact_Voice_Telephone:814-865-8792
Contact_Electronic_Mail_Address:datacommons@psu.edu
Metadata_Standard_Name:FGDC Content Standards for Digital Geospatial Metadata
Metadata_Standard_Version:FGDC-STD-001-1998
Metadata_Time_Convention:local time
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