GeCo3 is a DNA compressor that uses a neural network to do the mixing of experts.

Installation

Installation is available with conda.

conda install -y -c bioconda geco3

Build

GeCo3 depends on make and gcc.

cd src
make

NOTE: The default compilation options use micro-architecture dependent instructions, because GeCo3 greatly benefits from vector instructions. This means that due to the different floating point accuracies (e.g. fused multiply–add) the compressed file might not decompress with a binary compressed in a different computer or with a different compiler version or options. To ensure the file decompresses, use binaries (GeCo3 and GeDe3) that were compiled in the same environment.

Example usage

Reference free:

# Compression of file BuEb, using level 1, learning rate 0.06 and 8 hidden nodes
./GeCo3 -l 1 -lr 0.06 -hs 8 BuEb

# Decompression
./GeDe3 BuEd.co

Referential:

# Compression of file GG_C4 using as reference file PT_C4.
./GeCo3 -rm 20:500:1:35:0.95/3:100:0.95 -rm 13:200:1:1:0.95/0:0:0 -rm 10:10:0:0:0.95/0:0:0 -lr 0.03 -hs 64 -r PT_C4 GG_C4

# Decompression
./GeDe3 -r PT_C4 GG_C4.co

A complete description of the parameters can be read by invoking:

./GeCo3 -h
./GeDe3 -h

Export mixer to other compressors

Check the instructions and code in: https://github.com/cobilab/nn-expert-mixer

Citation

If you use GeCo3, please cite:

• Milton Silva, Diogo Pratas, Armando J Pinho, "Efficient DNA sequence compression with neural networks", GigaScience, Volume 9, Issue 11, November 2020, giaa119, https://doi.org/10.1093/gigascience/giaa119