Erik Garrison erik.garrison@bc.edu
Mengyao Zhao zhangmp@bc.edu
Last revision: 18/02/2014
SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages. We also provide a software that can do protein and genome alignment directly. Current version of our implementation is ~50 times faster than an ordinary Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically.
This is an extension of the main SSW implementation which allows access to the alignment score matrix, H, and E vectors. Using these features, we can extend the recurrence relation that defines the scores in the score matrix across junctions in the graph. Affine gaps and gaps overlapping junctions in the graph are also supported. Traceback is driven by storing the entire score matrix of each node (called the H matrix in the parlance of Farrar's original paper on the striped variant of the Smith-Waterman algorithm). Due to the memory requirements of this approach, it is currently only feasible to use GSSW in a local context (e.g. reference and reads in the tens of thousands of bases).
By constructing a graph using basic methods described in gssw.h, you can align
reads against the graph and obtain a graph mapping comprised of a graph "cigar"
describing the optimal alignment of the read across the nodes in the graph and
the starting position of the alignment on the first node. Nodes contain
(char*)s pointers which could be used to link to arbitrary metadata.
If you use this method the course of your work, please cite our article in PLOS One: SSW Library: An SIMD Smith-Waterman C/C++ Library for Use in Genomic Applications
This article does not cover the generalization of the method to work on partial order graphs, but rather the underlying structure and performance of the API used to score alignments against the graph.
The API files include gssw.h and gssw.c, which can be directly used by any C or C++ program. For the C++ users who are more comfortable to use a C++ style interface, an additional C++ wrapper is provided with the file ssw_cpp.cpp and ssw_cpp.h.
To use the C style API, please:
- Download gssw.h and gssw.c, and put them in the same folder of your own program files.
- Write
#include "gssw.h"into your file that will call the API functions. - The API files are ready to be compiled together with your own C/C++ files.
The API function descriptions are in the file ssw.h. One simple example of the API usage is example.c. The Smith-Waterman penalties need to be integers. Small penalty numbers such as: match: 2, mismatch: -1, gap open: -3, gap extension: -1 are recommended, which will lead to shorter running time.
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