Tool to align a genome sequence to a reference genome sequence using the Parasail library and Edlib Library.

C++ Implementation:

Dependencies:

1. Edlib
2. Parasail
3. g++
4. OpenMP
5. C++14

Usage: ./align [OPTIONS] --reads reads.fastq --control control_oligos.txt --output_file output_file.txt --parasail

-p, --print_alignment display best alignment for every read --version display version --help display this help and exit -r, --reads=FILE the ONT reads are in fastq FILE -c, --control=FILE the control oligos that are in a text FILE -f, --output_file=FILE the file to which the score will be output to --table_out the output to file will be in a tabular format including only the score and names of the read and the control --align_out the output to file will be in an alignment format which will include the read, control oligo and the SAM cigar --SAM_out the output to file will be a SAM file -t, --threads=NUM use NUM threads (default: 1) --parasail use the parasail library to generate the alignment sequence --edlib use the edlib library to produce the alignment sequence

Mandatory Fields:

1. --reads
2. --control
3. --parasail or --edlib

Compilation:

1. Clone/donwload the repository into your drive.
2. Change the working directory to the one you just cloned.
3. Make sure you have g++ and all dependencies installed.
4. Run "make"
5. Run the tool using the usage statement provided above.

Python Implementation:

Dependencies:

1. Parasail
2. pysam
3. python2.7

Compilation:

1. Run the command python "python align.py

Coded in Python and C++.