ReadMe

List of dependencies

The following is the complete list of dependencies and the version that have been tested:

To configure and build the project run the following commands from the root of the project:

./waf configure
./waf buid

To execute the alignment tool from the root of this repository:

./build/tools/alignment_tool

The previous command should print the help message of the tool. Example of usage are:

Local alignment with the score table in config.json

./build/tools/alignment_tool -i ./tests/Human-Mouse-BRCA2-cds.fasta -l -c ./tests/config.json

Global alignment with the score table in config.json

./build/tools/alignment_tool -i ./tests/Human-Mouse-BRCA2-cds.fasta -c ./tests/config.json

Global alignment using default scores ( +1 -1 -1 -5 )

./build/tools/alignment_tool -i ./tests/Human-Mouse-BRCA2-cds.fasta

To execute the alignment tool from the root of this repository:

./build/tools/suffixtree_tool

The previous command should print the help message of the tool. Examples of usage are:

Build and Print the SuffixTree as Dot file:

./build/tools/suffixtree_tool -i tests/s1.fasta --dot banana.dot

Build the SuffixTree and save to file the BWT and the Post Order

./build/tools/suffixtree_tool -i ./tests/s1.fasta --bwt banana.bwt --post banana.post

The directory output-files contains dumps of the outputs requested. The experiment folder contains the scripts used to generate them.

To execute the read mapping tool from the root of this repository:

./build/tools/read_mapping_tool

The previous command should print the help message of the tool. Examples of usage are:

Build and Print the SuffixTree as Dot file:

./build/tools/read_mapping_tool -g tests/Peach_reference.fasta -r tests/Peach_simulated_reads.fasta

To change the value of x, X, Y

./build/tools/read_mapping_tool -g tests/Peach_reference.fasta -r tests/Peach_simulated_reads.fasta -x <value> -X <value> -Y <value>

To give a different score table to the local alignment procedure:

./build/tools/read_mapping_tool -g tests/Peach_reference.fasta -r tests/Peach_simulated_reads.fasta -c tests/config.json

The directory output-files contains: