This is the Linux app named SOAP3-DP whose latest release can be downloaded as soap3-dp-2.3.172-cuda4.2-linux-AmazonEC2.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
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SOAP3-DP
DESCRIPTION
Latest Code on GitHub:
https://github.com/aquaskyline/SOAP3-dp
SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, CUSHAW2, GEM and GPU-based aligners BarraCUDA and CUSHAW, SOAP3-dp was found to be two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines.
Citation: Luo R, Wong T, Zhu J, Liu C-M, Zhu X, et al. (2013) SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner. PLoS ONE 8(5): e65632. doi:10.1371/journal.pone.0065632
Audience
Science/Research
User interface
Console/Terminal
Programming Language
C++, C
Categories
This is an application that can also be fetched from https://sourceforge.net/projects/soap3dp/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.
