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An assembler that has advantages of both string and de Bruijn graphs. First, the reads are decomposed adaptively only in error-prone regions. Second, each paired-end read is extended into a long read directly using an FM-index. The decomposed and extended reads are used to build an assembly graph. In addition, several essential components of an assembler were designed or improved. The resulting assembler was fully parallelized, tested, and compared with state-of-the-art assemblers using benchmark datasets. The results indicate that contiguity of StriDe is comparable with top assemblers on both short-read and long-read datasets, and the assembly accuracy is high in comparison with the others.

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Command line interface
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Department of Computer Science and Information Engineering, National Chung Cheng University, Taiwan

Funding source(s)

This work has been supported by MOST grants 104-2221-E-194-048-MY2 and 103-2923-E-194-001-MY3.

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