| # | |
| # This script calculates the depth of coverage and breadth of coverage for a given bam. | |
| # Outputs a dictionary containing the contig/chromosome names and the depth and breadth of coverage for each | |
| # and for the entire genome. | |
| # | |
| # If you optionally specify the name of the mitochondrial chromosome (e.g. mtDNA, chrM, chrMT) | |
| # The script will also generate breadth and depth of coverage for the nuclear genome AND the ratio | |
| # of mtDNA:nuclearDNA; which can act as a proxy in some cases for mitochondrial count within an individual. | |
| # | |
| # Author: Daniel E. Cook |
###a.) first create env with most dependencies:
conda create -n groomp2 python=2.7 matplotlib scipy bamm cython pillow pytables tempdir diamond hmmer pplacer mfqe orfm
###b.) obtain pip3 and use it to install singlem globally (while currently in the base environment OR any python3 environment)
sudo apt update
sudo apt install python3-pip
conda deactivate
conda deactivate # deactivate not only conda environment but also conda entirely (until you don't even see the base einvironment)