CoopPipe

Cooperative Pipeline for human viral genome reconstruction.

REPLICATION

To download CoopPipe in a Linux system, please run:

git clone https://github.com/mirakaya/CoopPipe.git
cd CoopPipe/src/
chmod +x *.sh

If Miniconda is not present, it can be downloaded and installed it with:

./CoopPipe.sh --miniconda

To install all of the tools necessary, please execute the pipeline with:

./CoopPipe.sh -i -t 4

To execute the whole pipeline, please type:

./CoopPipe.sh -r1 reads_forward.fq -r2 reads_reverse.fq
     --output out_analysis --threads 4 --memory 28        
     --tools HVRS/src --classifier falcon --all

CITATION

On using this software/method please cite:

• pending

ISSUES

For any issue let us know at issues link.

LICENSE

GPL v3.

For more information:

http://www.gnu.org/licenses/gpl-3.0.html