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JR-Assembler

Assembles de novo short read sequencing data. An assembler for the de novo assembly of large genomes using short sequence reads via jumping extension and read remapping. JR-Assembler extends a read by other whole reads, that is, it makes a jump. It uses a dynamic back trimming process to avoid extension termination due to sequencing errors. The tool achieves a superior performance on memory use and central processing unit time than most current assemblers when the read length is 150 bp or longer.

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JR-Assembler classification

JR-Assembler specifications

Software type:
Package/Module
Restrictions to use:
None
Computer skills:
Advanced
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux
Stability:
Stable

JR-Assembler distribution

versioning

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No versioning.

JR-Assembler support

Documentation

Maintainer

  • Arthur Chun-Chieh <>

Credits

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Publications

Institution(s)

Institute of Information Science, Academia Sinica, Taipei, Taiwan, China; Biodiversity Research Center, Academia Sinica, Taipei, Taiwan, China; Research Center for Information Technology Innovation, Academia Sinica, Taipei, Taiwan, China; Department of Computer Science and Information Engineering, National Taiwan Normal University, Taipei, Taiwan, China; Institute of Bioinformatics and Biosignal Transduction, National Cheng Kung University, Tainan, Taiwan, China; Department of Ecology and Evolution, The University of Chicago, Chicago, IL, USA

Funding source(s)

Supported by Academia Sinica and by National Science Council (Taiwan) Grants NSC99-2218-E-006-012, NSC99-3113- B-001-001, NSC 99-2321-B-001-041-MY2, and NSC 99-2621-B-001-003-MY3.

Link to literature

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