Multi-Locus Sequence Typing#
In this practical we will perform the genome typing by MLST analysis on the assembly of Klebsiella pneumoniae, using the contigs/scaffolds produced by the hybrid assembly in a previous tutorial.
Prepare our computing environment#
We will first run the appropriate srun command to book the computing cores (cpus) on the cluster.
Tip
You need to ask the teacher which partition to use !
srun -p SELECTED_PARTITION --cpus-per-task 2 --pty bash -i
You are now on a computing node, with computing 2 cpus reserved for you. That way, you can run commands interactively.
If you want to exit the srun interactive mode, press CTRL+D or type exit
Run the MLST program#
We should now identify our fasta file containing the contigs from the Unicycler hybrid assembly, produced from long and short reads. This will be the input file for mlst.
cd results
ls -l
Now we will run the MLST tool:
module load system/singularity/3.6.0
singularity run /path/to/mlst_singularity_container ...
mlst K2_unicycler_scaffolds.fasta > K2_unicycler_scaffolds_mlst.tsv
Tip
Ask the teacher for the MLST container path.
Once finished, you can exit the container by typing exit or press CTRL+D
Question
Check the output file. What is the sequence type of this strain?
Question
If the (hybrid) assemblies of the other Klebsiella pneumoniae strains are provided, try to make a loop to run the MLST analysis on all.