Parallel Positional Burrows-Wheeler Transform Algorithms

Publication and results : In Oxford Bioinformatics Advances (open access)

Dependencies

• This software depends on htslib for reading VCF/BCF files (version 1.12).
• This software depends on Google Benchmark for the benchmarks (version 1.5.2).

If the dependencies are already installed on the system the paths can be set accordingly in the Makefile. Else build the dependencies.

Build the dependencies

# htslib
git submodule update --init --recursive htslib
cd htslib
autoreconf -i
./configure
make
cd ..

# benchmark
git submodule update --init benchmark
cd benchmark
git clone https://github.com/google/googletest.git # benchmark depends on Google Test
cmake -E make_directory "build"
cmake -E chdir "build" cmake -DCMAKE_BUILD_TYPE=Release ../
cmake --build "build" --config Release
cd ..

Build and Run

make
make app # Generates application
make benchmark # Runs benchmark
make test # Runs unit tests

./app -h
Report matches example application
Usage: ./app [OPTIONS]

Options:
  -h,--help                   Print this help message and exit
  -f,--file TEXT              Input file name, default is stdio
  -o,--output TEXT            Output file name, default is stdio
  -t,--threads UINT           Number of threads
  -L,--length UINT            Length for long matches, 0 or undefined reports set maximal matches

Comparison with PBWT (Durbin 2014)

https://github.com/richarddurbin/pbwt

Note: For demonstration purposes this software only reads bi-allelic sites from VCF/BCF.

Report long matches

./pbwt -readVcfGT <input_file.vcf/bcf> -longWithin <length> > results.txt

./app -f <input_file.vcf/bcf> -L <length> -o results.txt -t <number of threads>

Report set maximal matches

./pbwt -readVcfGT <input_file.vcf/bcf> -maxWithin > results.txt

./app -f <input_file.vcf/bcf> -o results.txt -t <number of threads>