ECC

A clustering-based reference selection algorithm for reference-based compression on genome dataset. This program requires C++14 with g++ >= 5.3 and works on Linux

Download and Compile

git clone https://github.com/Tao-Tang/ECC.git
cd ECC
chmod +x bootstrap.sh
./bootstrap.sh
./configure
make

Execution

./ECC p -r result_name -s src_list -t thread_number (for reference-target pair selection)
./ECC c -r result_name -s src_list -t thread_number (for reference-target pair selection and compress data via hirgc)
./ECC d src_file (for decompression) 

• p for cluster a set of genome sequences
• c for cluster and compress a set of genome sequences
• d for decompress encoded file
• -r for the name of result file
• -s for the list of to be cluster sequences (each line will be read as a sequence name)
• -t for number of thread

Examples:

./ECC p -r my_archive -s file_list.txt -t 4
./ECC c -r my_archive -s file_list.txt -t 4
./ECC d my_archive

Example

cp ECC test
cd test
./ECC p -r a -s list.txt -t 4
nano ECC_a_pair.txt  (each line contains two files, first is the reference, second is target)
./ECC c -r a -s list.txt -t 4
ls -lh ECC_a.tar
./ECC d a
ls -lh ECC_a