How to run SARS-Cov-2 analysis in the computational infrastructure of INAB

Steps to run the analysis

1. Log in to the appropriate server

o 160.40.71.4

2 . Identify where your NGS results (.fastq files) are located

o e.g., /mnt/new_home/stamatopoulos_research/SARS_2025_05_21

3. Move to the your working directory

cd /work/covid19-runs

4. Create a new analysis directory

mkdir run-2025-10-23

5. Copy scripts to your analysis directory

cp *.sh run-2025-10-23

cp *.R run-2025-10-23

6. Move to the your new analysis directory

run-2025-10-23

7. Create a SampleList

You have to update with the right path to your fastq files.

ls -la /mnt/new_home/stamatopoulos_research/SARS_2025_05_21 | awk '{print $9}' | awk -F "_R" '{print $1}' | sort | uniq > SampleList

8. Remove samples that should not be analyzed

nano SampleList

In order to edit the SampleList use the following:

o Delete button: Removes one letter

o Ctrl + k: Removes a whole row

o Ctrl + o and Enter: Saves the modified SampleList

o Ctrl + x: Exits and returns to the terminal

9. Run the analysis

You have to update with the right path.

nohup bash runCOVID19.sh \
/mnt/new_home/stamatopoulos_research/SARS_2025_05_21 \
SampleList \
/work/covid19-runs/ref/NC_045512.2.fasta \
&

10. After the analysis is completed

Move your folder from /work to /mnt/new_home.

cd ..

rsync -r \
SARS_2025_05_21 \
/mnt/new_home/stamatopoulos_research