ONT_pilot_w_GDB_samples.md

@@ -597,6 +597,53 @@ sourmash plot ont_hybrid_bins_sourmash_comp --labels --pdf
 # downloaded the .csv file to the "Desktop" and used an additional Rscript for plotting
 ```
 
+##### dREP #####
+# checking to see if the bins are the same
+cd /scratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB
+mkdir bins
+cp /scratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/results/Binning/checkm_output/sample_list bins/.
+cd /scratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/bins
+
+# symlink files by renaming incrementally
+export i=1
+for f in `cat sample_list`
+do
+  for file in /scratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/results/Binning/"$f"/dastool_output/"$f"_DASTool_bins/*.fa
+  do
+     # Copy file to new location, safer than move in case you make a mistake
+     ln -s "$file" /scratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/bins/"$i"_"$f".fa
+
+   # Increment
+   let i=i+1
+   # Reset if exceeds 12
+   if [ $i -gt 500 ]
+   then
+      export i=1
+   fi
+  done
+done
+
+# removing some broken links
+rm 20_metaspades.fa 21_metaspades_hybrid.fa
+
+# Creating a new conda environment for drep
+srun -p interactive -t 4:00:00 --pty bash -i
+cd /scratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB
+conda create -n drep -c bioconda drep
+conda activate drep
+conda install -c bioconda fastani
+cd ~/apps/miniconda3/envs/drep/
+wget https://ani.jgi.doe.gov/download_files/ANIcalculator_v1.tgz
+tar -xzvf ANIcalculator_v1.tgz
+cp ANIcalculator_v1/ANIcalculator bin/.
+# testing drep installation
+dRep bonus testDir --check_dependencies
+
+# Running drep on the bins to see similarities
+cd /scratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/bins
+dRep compare drep_output -g ./*.fa
+```
+
 ##### QUAST #####
 - Testing assembly stats using quast
 ```