Skip to content

Latest commit

 

History

History
47 lines (39 loc) · 1.23 KB

README.md

File metadata and controls

47 lines (39 loc) · 1.23 KB
Raw

Blastn

An implementation of the basic local alignment search tool (Blast) for nucleotides. The goal of this project is to implement the Blastn algorithm in C++ and interop with an FPGA implementation of the Smith-Waterman algorithm to greatly accelerate the word extension stage of Blastn.

Project's New Location

New GitHub

Process

Blastn Process

Cloning

# HTTPS
$ git clone https://github.com/JacobLondon/Blastn.git --recurse-submodules

# SSH
$ git clone [email protected]:/JacobLondon/Blastn.git --recurse-submodules

Building and Running

Docker

Run docker build -t blastn . to create the environment with all necessary dependencies. Blastn will be placed under /root.

C++

See the C++ README.md

Dependencies

  • Python
    • python 3.6+
    • pip3
    • numpy
    • tqdm
  • C++
    • c++17
    • g++ 7.4+
    • GNU Make 4.2.1+

Members

Electrical and Computer Engineering Senior Project at California State Polytechnic University, Pomona

  • Alden Param
  • Alex Chan
  • Hmayak Apetyan
  • Jacob London
  • Simon Tutak
  • Sivaramakrishnan Prabakar

Advisors

  • Mostafa M. Hashim Ellabaan
  • Mohamed El-Hadedy