RandomStringAssembly

A final project from the course, Algorithm, requires to rebuild a string with its substrings. This implementation of sequence assembly is based on De Bruijn Graph.

Prerequisite

• MPICH 3.3.1
• PTHREAD
• C++ 11 supported

Build this project

1. mkdir build; cd build
2. cmake ../
3. make

Run the program

After executing the command above, a program named RandomStringAssembly is generated in the current directory. It should be run by the command of below:

mpiexec -np {the number of processes/hosts} ./RandomStringAssembly {the value of k of k-mer} {input folder} {the filename of the file of reads in the input folder}

. Multiple filenames can be splitted by white space following the argument of {input folder}.

For example:

• Command for running the program with 6 processes, k-mer with 79 characters, and input file named "reads" in the folder of "input".

mpiexec -np 6 ./RandomStringAssembly 79 "input" "reads"

• Command for running the program with 6 processes, k-mer with 79 characters, and input files named "reads1" and "reads2" in the folder of "input".

mpiexec -np 6 ./RandomStringAssembly 79 "input" "reads1" "reads2"