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C++ Blastn

Blastn implemented in C++. This implementation is designed to be the fast implementation which will interop with an FPGA implementation of the Smith-Waterman algorithm.

External Libraries

Building

Windows

  • Open Blastn.sln in Visual Studio 2019.
  • Visual Studio Setup
    • Open project properties
    • On the top, select Configuration: All Configurations
    • On the top, select Platform: All Platforms
    • Go to VC++ Directories
      • Select Include Directories -> Edit...
        • Click in the New Line button (shaped as a folder)
        • Enter $(ProjectDir)\include\parallel-hashmap
        • Click OK at the bottom
    • Go to C/C++ -> Optimization
      • Select Optimization: Maximum Optimization (Favor Speed) (/O2)
      • Select Favor Size or Speed: Favor Fast Code (/Ot)
    • Go to C/C++ -> Preprocessor
      • Select Preprocessor Definitions: <Edit...>
        • In definitions, enter _CRT_SECURE_NO_WARNINGS
        • This allows for the timestamp system to work as <ctime> is used.
    • Go to C/C++ -> Language
      • Select C++ Language Standard: ISO C++17 Standard (/std:c++17)
  • On the top, specify Release, x64, and press Ctrl + Shift + B to build.
  • The generated executable will be x64\Release\Blastn.exe.

Mac and Linux

  • In the cpp directory, run the make command.
  • The generated binary will be blastn.

Command Line Arguments

Argument Description Default Value
-query Path to query file data/SRR7236689--ARG830.fa
-subject Path to data file data/Gn-SRR7236689_contigs.fasta
-out Output file result.txt
-sep Query / subject seperator >
-word-length Word length 11
-sw-minscore Smith Waterman min score 20
-sw-match Smith Waterman match score 2
-sw-mismatch Smith Waterman mismatch score -3
-sw-gap Smith Waterman gap score -1
-dust-thresh Dust threshold 0.1
-dust-length Dust pattern length 3
-lambda E-value lambda constant 0.267
-kappa E-value kappa constant 0.041
-spacing Spacing between output columns 6
-fpga Score using an FPGA through UART COM4
-test Expects dust, extend, match, pairs, sequence, sw or smith waterman, sort, split NA