pythseq/mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

Introduction

Plasmids are mobile genetic elements (MGEs), which allow for rapid evolution and adaption of bacteria to new niches through horizontal transmission of novel traits to different genetic backgrounds. The MOB-suite is designed to be a modular set of tools for the typing and reconstruction of plasmid sequences from WGS assemblies.

The MOB-suite depends on a series of databases which are too large to be hosted in git-hub. They can be downloaded or updated by running mob_init or if running any of the tools for the first time, the databases will download and initialize automatically. However, they are quite large so the first run will take a long time depending on your connection and speed of your computer. The databases can be downloaded from figshare here: https://ndownloader.figshare.com/articles/5841882?private_link=a4c92dd84f17b2cefea6

MOB-init

On first run of MOB-typer or MOB-recon, MOB-init should run to download the databases from figshare, sketch the databases and setup the blast databases. However, it can be run manually if the databases need to be re-initialized.

% mob_init

MOB-cluster

This tool creates plasmid similarity groups using fast genomic distance estimation using MASH. Plasmids are grouped into clusters using single-linkage clustering and the cluster codes provided by the tool provide an approximation of operational taxonomic units OTU’s

MOB-recon

This tool reconstructs individual plasmid sequences from draft genome assemblies using the clustered plasmid reference databases provided by MOB-cluster.

MOB-typer

Provides in silico predictions of the replicon family, relaxase type, mate-pair formation type and predicted transferability of the plasmid

Installation

Requires

Python v. 3.6 +

Dependencies

blast+ v. 2.3.0 + circlator mash

Installation

% conda config --add channels defaults
% conda config --add channels conda-forge
% conda config --add channels bioconda
% conda install blast amos mash circlator

The MOB-suite uses the minimus2 pipeline from Circlator but there are some hardcoded links which need to be created in order for the tool to work correctly. After installing circlator and amos run the following as root.

% which show-coords 
using the path above as "conda-show-coords-path"
% ln -s conda-show-coords-path /usr/local/bin/show-coords

Pip

We recommend installing via bioconda but you can install it via pip using the command below

% pip3 install mob_suite

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

You can perform plasmid typing using a fasta formated file containing a single plasmid represented by one or more contigs. Do not include multiple unrelated plasmids in the file as they will be treated as a single plasmid.

# Basic Mode
% mob_typer --infile assembly.fasta --outdir my_out_dir

# Look for a file called mobtyper_(input_file)_report.txt
% cat my_out_dir/mobtyper_(input_file)_report.txt

Using MOB-recon to reconstruct plasmids from draft assemblies

This procedure works with draft or complete genomes and is agnostic of assembler choice but if unicycler is used, then the circularity information can be parsed directly from the header of the unmodified assembly.

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

### Full Mode
# In this mode, MOB-typer will be run on each identified plasmid grouping and will produce a summary report
% mob_recon --infile assembly.fasta --outdir my_out_dir --run_typer

Using MOB-cluster

Use this tool only to update the plasmid databases or build a new one and should only be completed with closed high quality plasmids. If you add in poor quality data it will severely impact MOB-recon

### Build a new database
% mob_cluster --mode build --infile plasmid.fasta --outdir output_directory

### Add a sequence to an existing database
% mob_cluster --infile update_sequences.fasta --ref_fasta_file original.fasta --ref_mash_db original.msh --ref_cluster_file original_clusters.txt 

### Test new plasmid database with MOB-recon
% makeblastdb -in path_to_plasmid_testing_db -dbtype nucl
% mash sketch -i path_to_plasmid_testing_db   <---- produces mash sketch file with format "path_to_plasmid_testing_db.msh"
% mob_recon --infile assembly.fasta --outdir my_out_dir --run_typer --plasmid_mash_db path_to_mash_testing_db --plasmid_db path_to_plasmid_testing_db

### Update MOB-suite plasmid databases
% mv new_mob_formated_db.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 

Output files

file	Description
contig_report.txt	This file describes the assignment of the contig to chromosome or a particular plasmid grouping
repetitive_blast_report	Summary information of contigs found to consist of nothing but a repetitive element
chromosome.fasta	Fasta file of all contigs found to belong to the chromosome
plasmid_(X).fasta	Each plasmid group is written to an individual fasta file which contains the assigned contigs
mobtyper_(input_file)_report.txt	Individual MOB-typer report files for each identified plasmid
mobtyper_aggregate_report.txt	Aggregate MOB-typer report files for all identified plasmid

MOB-recon contig report format

field id	description
file_id	Name of the input file
cluster_id	MOB-cluster type of reference match
contig_id	Unique identifier of the contig
contig_length	Length of the contig
circularity_status	Circular if Circlator or Unicycler find it to be circular, and incomplete if not
rep_type	Replicon types idenfied
rep_type_accession	Accessions of replicons identified
relaxase_type	Relaxase types identified
relaxase_type_accession	Accessions of relaxases identified
mash_nearest_neighbor	Mate-pair formation types identified
mash_neighbor_distance	Mate-pair formation type accessioons
repetitive_dna_id	Repetitive DNA match id
match_type	Repetitive element class
score	Blast bitscore of match
contig_match_start	Start of match on contig
contig_match_end	End of match on contig

MOB-typer report file format

field name	description
file_id	Name of the input file
num_contigs	Number of sequences identified in the file
total_length	Total number of bases in all sequences
gc	GC% of all sequences
rep_type(s)	Replicon types idenfied
rep_type_accession(s)	Accessions of replicons identified
relaxase_type(s)	Relaxase types identified
relaxase_type_accession(s)	Accessions of relaxases identified
mpf_type	Mate-pair formation types identified
mpf_type_accession(s)	Mate-pair formation type accessioons
orit_type(s)	Relaxase type of oriT sequence
orit_accession(s)	Accession for oriT
PredictedMobility	Mobility prediction for the plasmid (Conjugative, Mobilizable, Non-mobilizable)
mash_nearest_neighbor	Accession of closest database match
mash_neighbor_distance	Mash distance from query to match
mash_neighbor_cluster	MOB-cluster type of reference match

Contact

James Robertson - [email protected]

License

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this work except in compliance with the License. You may obtain a copy of the License at:

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.