3.1.9

MOB-suite container

Main tool: mob_suite

Code repository: https://github.com/phac-nml/mob-suite

Additional tools:

• blast+ : 2.12.0+
• mash : 2.3

Basic information on how to use this tool:

• executable: mob_init, mob_cluster, mob_recon, mob_typer
• help: -h, --help
• version: -V, --version
• description: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

Additional information:

The MOB-suite depends on a series of databases which is not included in the container. They can be downloaded and updated by running mob_init or can be manually downloaded from here.

Full documentation:

Robertson, J., & John. (2018). MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microbial Genomics, 4(8). https://doi.org/10.1099/mgen.0.000206 ‌

Example Usage

Using MOB-typer to perform replicon and relaxase typing of complete plasmids and predict mobility

# Single plasmid
mob_typer --infile assembly.fasta --out_file sample_mobtyper_results.txt

# Multiple independant plasmids
% mob_typer --multi --infile assembly.fasta --out_file sample_mobtyper_results.txt

Using MOB-recon to reconstruct plasmids from draft assemblies

# Basic Mode
mob_recon --infile assembly.fasta --outdir my_out_dir

# User sequence mask
mob_recon --infile assembly.fasta --outdir my_out_dir --filter_db filter.fasta

# Autodetected close genome filter
mob_recon --infile assembly.fasta --outdir my_out_dir -g 2019-11-NCBI-Enterobacteriacea-Chromosomes.fasta

Using MOB-cluster

# Build a new database
mob_cluster --mode build -f new_plasmids.fasta -p new_plasmids_mobtyper_report.txt -t new_plasmids_host_taxonomy.txt --outdir output_directory

# Add a sequence to an existing database
mob_cluster --mode update -f new_plasmids.fasta -p new_plasmids_mobtyper_report.txt -t new_plasmids_host_taxonomy.txt --outdir output_directory -c existing_clusters.txt -r existing_sequences.fasta

# Update MOB-suite plasmid databases
cp output_directory/clusters.txt
mv output_directory/updated.fasta mob_db_path/ncbi_plasmid_full_seqs.fas
makeblastdb -in mob_db_path/ncbi_plasmid_full_seqs.fas -dbtype nucl
mash sketch -i mob_db_path/ncbi_plasmid_full_seqs.fas