Plasmids detection#

We will now search for plasmids features in the assembled scaffolds/contigs to detect which ones could have originated from a plasmid.

For this, we will use 2 different tools:

• PlasmidFinder, developed at the Center for Genomic Epidemiology, like many other tools for bacterial genomics analysis. It searched for known plasmids and provide the replicon type.

• Platon, a tool that detects plasmid-borne contigs within bacterial draft (meta) genomes assemblies. Therefore, Platon analyzes the distribution bias of protein-coding gene families among chromosomes and plasmids. This analysis is complemented by comprehensive contig characterizations followed by heuristic filters. Platon depends on a custom database based on MPS, RDS, RefSeq Plasmid database, PlasmidFinder db as well as manually curated MOB HMM models from MOBscan, custom conjugation and replication HMM models and oriT sequences from MOB-suite.

Prepare our computing environment#

We will first run the appropriate srun command to book the computing cores (cpus) on the cluster.

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

Practical#

First, you need to identify in your results directory the fasta file corresponding to the unicycler hybrid assembly.

cd results
ls -l

PlasmidFinder#

We will use the PlasmidFinder container that has all tools needed for running PlasmidFinder

module load system/singularity/3.6.0

singularity shell path/to/plasmidfiner_container

mkdir K2_plasmidfinder

plasmidfinder.py -i K2_unicycler_scaffolds.fasta -o K2_plasmidfinder -p /path/to/PF_DB -mp blastn -x

Once finished, you can exit the container by typing exit or press CTRL+D

Platon#

We will use a second tool for detecting sequences of plasmidic origin: Platon

module load system/singularity/3.6.0

singularity shell path/to/platon_container

platon --db path/to/databases/platon/db/ -t 4 -o K2_unicycler_platon_accu K2_unicycler_scaffolds.fasta