SOAPnuke pipeline

SOAPnuke specifications


Unique identifier OMICS_25036
Name SOAPnuke
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Windows
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.6.2
Stability Stable
Requirements boost, zlib, log4cplus, openssl, R
Maintained Yes



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  • person_outline Qiang Chen <>
  • person_outline Lin Fang <>
  • person_outline Yuxin Chen <>
  • person_outline Yongsheng Chen <>
  • person_outline Chunmei Shi <>

Publication for SOAPnuke

SOAPnuke citation

PMCID: 5648118

[…] usa). finally, the libraries were sequenced on an illuminahiseq™ 2000 platform., the original image data were transformed into sequence data via base calling. these raw reads were filtered using the soapnuke program, as previously described [20], and the remaining “clean” reads were used in the downstream bioinformatics analyses. the quality of the clean reads data was assessed using base […]

SOAPnuke institution(s)
BGI-Shenzhen, Shenzhen, China; Geneplus-Beijing, Beijing, China; Department of Oncology, Fujian Medical University Union Hospital, Fuzhou, China; Fujian Key Laboratory of Translational Cancer Medicine, Fuzhou, China; Department of Stem Cell Research Institute, Fujian Medical University Stem Cell Research Institute, Fuzhou, China; Collaborative Innovation Center of High Performance Computing, National University of Defense Technology, Changsha, China; Intel China Ltd., Shanghai, China; Guangdong Provincial Hospital of Chinese Medicine, Guangzhou, China; Department of Surgery, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China; James D. Watson Institute of Genome Sciences, Hangzhou, China
SOAPnuke funding source(s)
Supported by Collaborative Innovation Center of High Performance Computing, Critical Patented Project of the Science & Technology Bureau of Fujian Province, China (Grant No. 2013YZ0002-2) and the Joint Project of Natural Science and health Foundation of Fujian Province, China (Grant No.2015J01397).

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