Parallel Reference-based Compression of Paired-end Genomics Read Datasets

Dependencies

• g++ with support for c++11
• libbsc software (included in this project)

Compilation

Inside refcom directory,

cd libbsc
make
cd ..
make

Execution

Compression

Inside refcom directory,

./REFCOM --operation compression     \
--ref_file_name <REFERENCE_FILE>     \
--rd1_file_name <INPUT_FASTQ_FILE_1> \
--rd2_file_name <INPUT_FASTQ_FILE_2> \
--com_file_name <COMPRESSION_OUTPUT> \
--thread_count <THREAD_COUNT>

Decompression

Inside refcom directory,

./REFCOM --operation decompression    \
--ref_file_name <REFERENCE_FILE>      \
--com_file_name <COMPRESSION_OUTPUT>  \
--rd1_file_name <OUTPUT_FASTQ_FILE_1> \
--rd2_file_name <OUTPUT_FASTQ_FILE_2>

<REFERENCE_FILE> and <COMPRESSION_OUTPUT> are the same for both compression and decompression

Decompression uses the same number of threads as compression