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SOAPdenovo

Provides a short-read assembly method that can build a de novo draft assembly for the human-sized genomes. SOAPdenovo is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost-effective way. SOAPdenovo is made up of six modules that handle read error correction, de Bruijn graph (DBG) construction, contig assembly, paired-end (PE) reads mapping, scaffold construction, and gap closure. The major last improvements of SOAPdenovo are: i) enhancing the error correction algorithm, ii) providing a reduction in memory consumption in DBG constructions, iii) resolving longer repeat regions in contig assembly, iv) increasing assembly length and coverage in scaffolding and v) improving gap closure.

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SOAPdenovo classification

SOAPdenovo specifications

Software type:
Package/Module
Restrictions to use:
None
Programming languages:
C, C++
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Interface:
Command line interface
Operating system:
Unix/Linux, Mac OS
License:
GNU General Public License version 2.0
Version:
2.0
Requirements:
GCC

SOAPdenovo distribution

versioning

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SOAPdenovo support

Documentation

Maintainer

  • Jun Wang <>

Credits

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Publications

Institution(s)

BGI HK Research Institute, Tai Po Industrial Estate, Hong Kong; HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department of Computer Science, University of Hong Kong, Pokfulam, Hong Kong; School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, China; School of Computer Science, National University of Defense Technology, Kaifu District, Changsha, Hunan, China

Funding source(s)

The project was supported by the State Key Development Program for Basic Research of China-973 Program (2011CB809203), National High Technology Research and Development Program of China-863 program (2012AA02A201), the National Natural Science Foundation of China (90612019), the Shenzhen Key Laboratory of Trans-omics Biotechnologies (CXB201108250096A), the Shenzhen Municipal Government of China (JC201005260191A and CXB201108250096A), and partially supported by RGC General Research Fund 10612042.

Link to literature

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