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Metaome Stats: Calculating denovo assembly statistics from metaomes

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Installing

  • pip installation
    pip install MetaomeStats

  • conda installation
    conda install -c bioconda MetaomeStats

  • source (github)

git clone https://github.com/raw-lab/metaome_stats
cd metaome_stats
python setup.py

Usage examples

countAssembly.py -i 100 --fasta ecoli_Miseq_Assembly.fa

Main options:

usage: countAssembly.py -i INTERVAL -f FASTA [-r REF] [-s SIZE] [-h]

required arguments:
  -i INTERVAL, --interval INTERVAL
                        interval size in # of residues
  -f FASTA, --fasta FASTA
                        fasta file or folder

optional arguments:
  -r REF, --ref REF     reference genome
  -s SIZE, --size SIZE  reference genome size
  -h, --help

Input formats

  • FASTA files without quality scores (.fasta, .fa, .fna, .ffn format)

Citing Metaome Stats

If you are publishing results obtained using Metaome Stats, please cite:

CONTACT

The informatics point-of-contact for this project is Dr. Richard Allen White III.
If you have any questions or feedback, please feel free to get in touch by email.
Dr. Richard Allen White III: mailto
Jose Figueroa: mailto
Or open an issue.