parallel-pairwise

Attempt to brute-force sourmash signatures pairwise comparisons. Result is written in a csv files.

Build

cmake -Bbuild -DCMAKE_BUILD_TYPE=RELEASE
cmake --build build -j 4
# ./build/pairwise <sigs_directory> <threads> <kSize> <output>"

Clustering

First: install dependecies

pip install -r requirements.txt

Second: run clustering

python cluster_it.py --csv CSV --cutoff CUTOFF --output OUTPUT

Example:

./build/pairwise test_data 16 51 pairwise_test_data
python cluster_it.py --csv pairwise_test_data.csv --cutoff 10 --output clusters_test_data.txt