By providing a folder containing either metagenome assembled genomes (MAGs) or the contigs generated from an assembly this program will output a file in TSV format summarizing GC%, tetranucelotide frequency, codon frequency, depth (optional), and the taxanomic group (optional) matched to each contig.
git clone https://github.com/pavia27/Barbizon.git
cd Barbizon
bash setup.sh
source activate barbizon
*Do not worry about the dependencies after conda installation. Just enter source deactivate when finished using the program.
Print out the help screen :
./barbizon.py -h
For quick usage to generate a tsv of GC%, tetranucleotide identity, and codon usage :
./barbizon.py -b MAGS/ -o test_MAG_set
To include depth information :
./barbizon.py -b MAGS/ -o test_MAG_set --bam optional.bam.sorted
./barbizon.py -b MAGS/ -o test_MAG_set --bam optional_1.bam.sorted,optional_2.bam.sorted,optional_3.bam.sorted
To include taxonomic information : Please provide a reference protein dataset for use by CAT. Below are commands for downloading the database:
wget tbb.bio.uu.nl/bastiaan/CAT_prepare/CAT_prepare_20210107.tar.gz
tar -xvzf CAT_prepare_20210107.tar.gz
Move CAT_prepare_20210107 directory to the Barbizon directory
./barbizon.py -b example_MAGS/ -o test_MAG_set --bam optional.bam.sorted -t 10 -c TRUE