Mapping long reads to large reference databases

This is a project for the bioinformatics course on FER (http://www.fer.unizg.hr/en/course/bio).

Paper describing the implemented algorithm can be found here, and its C++ implementation is on GitHub. The C++ implementation seems to differ a bit from the paper description as the authors have improved the algorithm over time.

Installation

The dependencies for this program are all bundled in ./pom.xml and therefore will automatically be downloaded; you only need to have Maven installed on you machine. Running mvn package from project root should be enough to install the program under ./target.

Running the program

The program expects two parameters, reference and query read in FASTA file format (provided FASTA files should not contain any comments).

You can run the program by issuing the command:

java -jar ./target/bioinf-1.0-SNAPSHOT.jar [reference.fa] [query.fa]

If everything goes well, read data should be output to ./[query-location].fa-out.txt (note that the FASTA file name is just query filename suffixed by -out.txt.

Testing

If you would like to run a sample test of the functionality, under ./helpers there are two simple bash scripts; you can first generate queries using simulate.sh like so:

./helpers/simulate.sh read

This will create sample queries under ./genomes/clostridium/queries. You can test the program (after it's been built using mvn package) on every one of them by running:

./helpers/run.sh

This will produce outputs in the root directory.