MIDAS consists of four primary steps: the species step, the genes step, the snps step, and then merging the output of each of these processes over all relevant hosts.
Below, we provide example .bash scripts which accomplish each of these steps; however, individual clusters or machines might require slightly different setups.
An example .bash script which runs this step is located at ../Scripts/MIDAS_species.bash.
Supposing that your data consists of multiple time points, you may wish to consider a list of species per host taking into account all of the time points.
'../Scripts/construct_species_union.py' is a python script accepts an indir containing all *species_profile.txt files output by the species step to output a species_union.txt at a specified outprefix.
An example .bash script which runs this step is located at ../Scripts/MIDAS_genes.bash.
An example .bash script which runs this step is located at ../Scripts/MIDAS_snps.bash.
The merge step is performed over each of the outputs from the previous steps. Example bash scripts can be found at: