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Summary: The Smith Waterman (SW) algorithm, which produces the optimalpairwise alignment between two sequences, is frequently used as a key componentof fast heuristic read mapping and variation detection tools, but currentimplementations are either designed as monolithic protein database searchingtools or are embedded into other tools. To facilitate easy integration of thefast Single Instruction Multiple Data (SIMD) SW algorithm into third partysoftware, we wrote a C/C++ library, which extends Farrars Striped SW (SSW) toreturn alignment information in addition to the optimal SW score. Availability:SSW is available both as a C/C++ software library, as well as a stand alonealignment tool wrapping the librarys functionality athttps://github.com/mengyao/Complete- Striped-Smith-Waterman-Library Contact:marth@bc.edu

SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications