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SOAP3-DP

Fast, Accurate and Sensitive GPU-based Short Read Aligner

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BSD Linux

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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

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Additional Project Details

Languages

English

Intended Audience

Science/Research

User Interface

Console/Terminal

Programming Language

C++, C

Registered

2013-05-31
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