For use in differential coverage binning of metagenomic contigs into metagenome-assembled genomes (MAGs).
Script takes individual metagenome depth profiles generated with different read sets and outputs three summary depth profiles:
- Coverage in the given sample ("$sample"_depth-single.txt)
- Coverage across related samples (e.g., from the same site) based on provided mapping file ("$sample"_depth-all.txt)
- Coverage across all provided samples ("$sample"_depth-all.txt)
The depth profiles need to have been generated with the metaBAT (https://bitbucket.org/berkeleylab/metabat/src/master/) command "jgi_summarize_bam_contig_depths" and have the name structure: "$sample"_"$reads".depth.txt.
The script also requires a tab-seperated mapping file with a site name in the first column, and sample name in the second column that corresponds to the sample names in the initial profile file names.
Example:
python scripts/make_depth_summaries.py \
-sample "Sample_name" \
-map "Site-to-sample_map_file.tsv" \
-depth "Folder_with_all_depth_profiles" \
-out "Output_folder"