SOAP specifications
- Unique identifier:
- OMICS_00688
- Software type:
- Toolkit/Suite
- Restrictions to use:
- None
- Output format:
- Tab-delimited text, SAM
- Programming languages:
- C, C++, Perl
- Computer skills:
- Advanced
- Stability:
- Beta
- Wikipedia:
- https://en.wikipedia.org/wiki/Short_Oligonucleotide_Analysis_Package
- Name:
- Short Oligonucleotide Analysis Package
- Interface:
- Command line interface
- Input format:
- FASTA
- Operating system:
- Unix/Linux
- Parallelization:
- CUDA
- Version:
- 3.0
- Maintained:
- Yes
versioning
No versioning.
SOAP distribution
download
SOAP support
Maintainers
- SOAP3 <>
- Tak-Wah Lam <>
- Yingrui Li <>
- Ruiqiang Li <>
forum
No open topic.
Credits
Publications
-
(Liu et al., 2012)
SOAP3: ultra-fast GPU-based parallel alignment tool for short reads.
Bioinformatics.
PMID: 22285832 -
(Li et al., 2009)
SOAP2: an improved ultrafast tool for short read alignment.
Bioinformatics.
PMID: 19497933 -
(Luo et al., 2013)
SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner.
PLoS One.
PMID: 23741504 DOI: 10.1371/journal.pone.0065632 -
(Li et al., 2008)
SOAP: short oligonucleotide alignment program.
Bioinformatics.
PMID: 18227114 DOI: 10.1093/bioinformatics/btn025
Institution(s)
HKU-BGI Bioinformatics Algorithms and Core Technology Research Laboratory & Department of Computer Science, University of Hong Kong, Hong Kong, China; School of Computer Science, National University of Defense Technology, Changsha, Hunan, China; BGI-Shenzhen, Shenzhen, Guangdong, China; Peking-Tsinghua Center for Life Sciences, Biodynamic Optical Imaging Center and School of Life Sciences, Peking University, Beijing, China; Department of Computer Sciences, University of Wisconsin-Madison, Madison, Wisconsin, USA
Funding source(s)
Supported by RGC General Research Fund 10612042, Hong Kong ITF Grant GHP/011/12 and the GRF Grant HKU-713512E.
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