NanoMapper

A Mapping tool using gapped minimizer and BWT FM-index

Prerequisites:

API:

We have used SDSL-lite for fm-index. So, you need to install that first. To install that, you have to do the following:

• Make sure you have an updated cmake build system.

• Make sure your g++ version >= 4.9 and clang version >= 3.2

• Give the following commands in your terminal:

    git clone https://github.com/simongog/sdsl-lite.git
    cd sdsl-lite
    ./install.sh
  

OS:

• 64-bit unix based operating system (Linux or Mac OS X).

Instructions:

• To get NanoMapper in your PC:

    git clone https://github.com/enamcse/NanoMapper.git && cd NanoMapper
  

• To compile the current version, give the following command from the current directory:

    g++ -o NanoMapper -std=c++11 -O3 -DNDEBUG -I ~/include -L ~/lib ./Minimizer\ FM-index\ Merged\ Approach/Main_minimizer.cpp -lz -lsdsl -ldivsufsort -ldivsufsort64
  

• To run a demo, give the following command:

    ./NanoMapper './DataSet/synthetic_reference.fasta' './DataSet/synthetic_reads.fasta' 14 24 2 './Results/Merged_enhanced_res.txt' >> './Results/Summary.txt'
  

Developer

Enamul Hassan and Md. Khairullah Gaurab under the direction of Ruhul Amin Shajib Sir

Contact Information

Enamul Hassan : enamsustcse@gmail.com

Md. Khairullah Gaurab : mkgaurabsarkar@gmail.com