SOAPdenovo protocols

SOAPdenovo specifications

Information


Unique identifier OMICS_00031
Name SOAPdenovo
Alternative name SOAPdenovo2
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 2.0
Stability Stable
Requirements GCC
Maintained Yes

Subtool


  • GapCloser

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Versioning


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Documentation


Maintainers


  • person_outline Jun Wang <>
  • person_outline SOAPdenovo Team <>

Additional information


https://sourceforge.net/projects/soapdenovo2/

Publications for SOAPdenovo

SOAPdenovo IN pipelines

 (82)
2018
PMCID: 5905561
PMID: 29444297
DOI: 10.1093/gigascience/giy006

[…] of 10.8 and 11.8 gb raw data for h. cichorii and h. phaleratus were obtained, respectively (table 1). before assembly, strict quality control was performed using soapfilter (v2.2), a package from soapdenovo2 (soapdenovo2, rrid:scr_014986) [23], removing adaptor contaminated and duplicate reads produced from pcr amplification and condetri (condetri, rrid:scr_011838) [24] to trimming […]

2018
PMCID: 5905561
PMID: 29444297
DOI: 10.1093/gigascience/giy006

[…] 11.8 gb raw data for h. cichorii and h. phaleratus were obtained, respectively (table 1). before assembly, strict quality control was performed using soapfilter (v2.2), a package from soapdenovo2 (soapdenovo2, rrid:scr_014986) [23], removing adaptor contaminated and duplicate reads produced from pcr amplification and condetri (condetri, rrid:scr_011838) [24] to trimming low-quality bases, […]

2018
PMCID: 5945678
PMID: 29748645
DOI: 10.1038/s41598-018-25826-6

[…] a total of 542,339,262 raw paired-end reads were generated, out of which, a total of 446,580,418 clean reads were used for assembly (supplementary table s2). the de novo assembly was performed using soapdenovo assembler, which was run at different k-mer size ranging from 19 to 29 mers with read-length of 33 bp. a total of 91,765 transcripts with an average length of 903.39 bp, n50 value 1,427 […]

2018
PMCID: 5946948
PMID: 29688346
DOI: 10.1093/gigascience/giy046

[…] estimated that the entire genome comprised 806 mb, with a gc (guanine-cytosine) content of 40.8% (additional files: figs. s2, s3, and table s2)., the monopterus genome was de novo assembled with the soapdenovo software [16]. soapdenovo employs the de bruijn graph algorithm to simplify assembly and reduce computational complexity. low-quality reads were filtered out, and potential sequencing […]

2018
PMCID: 5946948
PMID: 29688346
DOI: 10.1093/gigascience/giy046

[…] genome comprised 806 mb, with a gc (guanine-cytosine) content of 40.8% (additional files: figs. s2, s3, and table s2)., the monopterus genome was de novo assembled with the soapdenovo software [16]. soapdenovo employs the de bruijn graph algorithm to simplify assembly and reduce computational complexity. low-quality reads were filtered out, and potential sequencing errors were removed […]

SOAPdenovo 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
SOAPdenovo 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.

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