Utilities and workflows for examining (metagenome) binning results.
(A "midgie" is a trash heap, and a "midgie raker" is someone who combs through trash heaps looking for good stuff.)
midgie-raker is organized as a snakemake workflow, with the top level
rules being in Snakefile.
First, edit config.yaml and databases.yaml appropriately for your system
and bins.
Then, snakemake -j 64 rename will get you started.
Start with sketch-raw, which takes a bunch of FASTA files of MAGs
and sketches them with sourmash scripts manysketch.
Then, move on to rename, which takes the sketches, builds taxonomic
profiles of them with gather against GTDB, and renames them consistently.
*Next, run decontam, which profiles the sketches against eukaryotes + GTDB,
and flags bins that contain substantial amounts of multi-class content.
Then, run min-set-cov. This profiles the bins against GTDB,
determining the size of the minimum set cover for each bin, and also
calculating the novelty in each bin.
Finally, the bin-coverage code will calculate coverage histograms
for selected MAG x metagenome comparisons.