TGC - Thousands Genome Compressor

Thousands Genome Compressor is a tool to estimate the boundaries of compression ratio for human genome compression. It can be also used as a very effective tool for compression Variant Call Format (VCF) files.

TGC is composed of several programs that were used in our experiments on the genomes from the 1000 Genomes project. A description of the tool can be found in TGC description.

We were able to compress the genomes from the 1000GP about 15,500 times. More details can be found in our paper pointed below.

Getting Started

# Clone repository
git clone https://github.com/refresh-bio/tgc.git
# Build 
cd tgc
cd src
make
cd ..
# Repeat experiments described in the publication
./run -abcdefgijklcd tgc

Developers

The TGC algorithm was invented by Sebastian Deorowicz, Szymon Grabowski, and Agnieszka Danek. The implementation is by Agnieszka Danek and Sebastian Deorowicz.

Citing

Deorowicz, S., Danek, A., Grabowski, Sz. (2013) Genome compression: a novel approach for large collections, Bioinformatics; 29(20):2572–2578