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EBARDenovo | De novo assembly of RNA-Seq with chimera-detection

Assembles paired-end RNA-Seq data. EBARDenovo is based on a bi-directional expansion method using paired-end RNA-Seq data to guide the transcriptome assembly. The software is suited for detecting chimeric reads, created by natural gene fusion or sequence recombination, and assembly errors. Its outputs can be used for further analyses such as the identification of RNA editing sites and gene fusion candidates.

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Thomas

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Great tool, good accuracy.

EBARDenovo forum

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EBARDenovo classification

EBARDenovo specifications

Unique identifier:
OMICS_01317
Software type:
Application/Script, Package/Module
Restrictions to use:
Academic or non-commercial use
Operating system:
Unix/Linux, Mac OS, Windows
License:
Common Public License Version 1.0
Version:
2.0.1
Maintained:
Yes
Name:
Extension, Bridging And Repeat-sensing Denovo
Interface:
Command line interface
Output data:
Some files containing information about the sequences, the aligned reads in each contig, the alignment of used pairs and the plot of sequence coverage.
Programming languages:
C#
Computer skills:
Advanced
Stability:
Stable

EBARDenovo distribution

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EBARDenovo support

Maintainers

  • Cheng-Yan Kao <>
  • Hsueh-Ting Chu <>
  • Theresa Tsao <>

Credits

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Publications

Institution(s)

Department of Biomedical informatics, Asia University, Taichung, Taiwan; Department of Computer Science and Information Engineering, Asia University, Taichung, Taiwan; BCCDC Public Health Microbiology & Reference Laboratory, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Institute of Biotechnology, National Taiwan University, Taipei, Taiwan; Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, Taiwan; Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan; National Research Institute of Chinese Medicine, Taipei, Taiwan; Department of Information Management, Kainan University, Taoyuan, Taiwan; Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan

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