https://github.com/cobilab/geco3
An efficient DNA sequence compressor using Neural Networks
https://github.com/cobilab/geco3
compression-algorithm dna-sequences neural-networks
Last synced: 22 days ago
JSON representation
An efficient DNA sequence compressor using Neural Networks
- Host: GitHub
- URL: https://github.com/cobilab/geco3
- Owner: cobilab
- License: gpl-3.0
- Created: 2020-04-05T09:47:50.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2023-01-25T14:54:44.000Z (over 3 years ago)
- Last Synced: 2024-01-21T05:40:22.693Z (over 2 years ago)
- Topics: compression-algorithm, dna-sequences, neural-networks
- Language: C
- Homepage:
- Size: 366 KB
- Stars: 12
- Watchers: 3
- Forks: 8
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
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