ONT_pilot_w_GDB_samples.md

@@ -496,6 +496,32 @@ mv -vf cd-hit cd-hit_non_mod_basecalled   # renamed the folder since it was run
 - For example: since we used two mappers bwa-mem and minimap for the reads, we binned each sample separtely based on the mapper
 - Additionally, we needed to merge bam files for the "hybrid"-binning, so we compared bins using [sourmash](https://github.com/dib-lab/sourmash) and compared assemblies using [quast](https://github.com/ablab/quast)
 
+##### QUAST - 2019_GDB #####
+- Like any good experiment, sometimes the basics are key evaluators of the data
+- To address this, used (meta)[QUAST](https://github.com/ablab/quast) to assess how the assemblies look
+```
+# Testing assembly stats using quast on the 2019_GDB "methylation-aware" data
+srun -p interactive -t 4:00:00 --pty bash -i    # interactive session
+conda activate quast
+cd /mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/
+mkdir quast_methylation_aware
+cd quast_methylation_aware
+ln -s  ../results/assembly/*.fa .
+
+metaquast.py --max-ref-number 0 --threads 24 *fa -o methylation_2019_quast_results
+
+# Testing assembly stats using quast on the 2019_GDB "non_mod" basecalled data
+srun -p interactive -t 4:00:00 --pty bash -i    # interactive session
+conda activate quast
+cd /mnt/lscratch/users/sbusi/ONT/cedric_ont_basecalling/2019_GDB/
+mkdir quast_non_mod
+cd quast_non_mod
+ln -s ../non_methylation_aware_results/assembly/*.fa .
+
+metaquast.py --max-ref-number 0 --threads 24 *fa -o non_mod_2019_quast_results
+# downloaded both the folders to desktop at ~/Documents/Nanopore_ONT/.
+```
+
 ##### SOURMASH #####
 - To check if the bins across different metaspades_hybrid 'bam' files are similar 
 - to decide whether to go with sr_bam or merged_bam files