POSTME : POSTprocessing MEtagenomics assembly with hybrid data by highly precise scaffolding

To use the tool, use the following command(assuming illuminaContigs.fasta and pacbioReads.fasta are in workingDirectory). The output file is improved.fasta

python postme.py \
    -o workingDirectory/ \
    -a mummerPath/ \
    -c illuminaContigs.fasta \
    -r pacbioReads.fasta

Unit tests are continuously tested on Travis CI and the current build status is

1. Clone POSTME

    git clone https://github.com/kakitone/postme.git
   

2. Install dependency, you can do it through virtualenv

    pip install virtualenv
    source venv/bin/activate
    pip install numpy scipy biopython matplotlib
   

3. To make sure you have installed all the dependency,

    python postme/myunittest.py
   

4. You can now run POSTME.