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PlaScope

A targeted approach to assess the plasmidome of bacteria.

If you use this tool, please cite : G. Royer, J.-W. Decousser, C. Branger, M. Dubois, C. Médigue, E. Denamur, D. Vallenet. PlaScope: a targeted approach to assess the plasmidome from genome assemblies at species level. Microbial Genomics, 2018 Sep;4(9).

And don't forget the publications related to its dependencies :

  • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19:455–477
  • Kim D, Song L, Breitwieser FP, Salzberg SL. Centrifuge: rapid and sensitive classification of metagenomic sequences. Genome Res 2016;26:1721–1729

Tell me more about PlaScope

This method enables you to classify contigs from a WGS assembly according to their location (i.e. plasmid or chromosome). It is based on a smart tool called Centrifuge, initially developed as a metagenomic classifier. We propose here an application on E. coli plasmidome, with a specific database build on one hand on completely finished genomes of E. coli from the NCBI, and on the other hand on a custom plasmid database. In fact 3 databases of plasmid have been merged together :

We also propose a Klebsiella database that has been evaluated on a clinical dataset of 12 Klebsiella pneumoniae strains.

We think that this method can easily be applied to other bacterial species since you have got enough reference data (e.g. Staphylococcus aureus, Enterococcus sp. ...).

Installation

Dependencies

You must install these dependencies before you start :

  • SPAdes 3.10.1 or later if you want to run the assembly (= mode 1) (header of contigs must be the same as in version 3.10.1, e.g >NODE_1_length_506801_cov_117.065)
  • Centrifuge 1.0.3

Installation

PlaScope is essentially a wrapper script (called plaScope.sh) around SPAdes and Centrifuge. It's written in bash and awk and should work on Linux and Mac OS X both with GNU awk and BSD awk.

To install it, simply download the sources and decompress them. Don't forget to add the location of plaScope.sh to your PATH.

Installation with BioConda

The easiest way to install PlaScope and its dependencies is through BioConda. Once you have created and activated a conda environment, simply type:

$ conda install plascope

Note that several versions of awk are available in conda so you can further control the environment.

Usage with the IFB Cloud

Another way to use PlaScope is through the IFB Cloud. Just create an account and launch the PlaScope appliance.

Usage

You can choose between two modes:

  • Mode 1: SPAdes assembly then contig classification
  • Mode 2: contig classification only (if you already assembled your genome with SPAdes or Unicycler)
$ ./plaScope.sh -h
usage: plaScope.sh [OPTIONS] [ARGUMENTS]

General options:
  -h, --help		display this message and exit
  -v, --version		display version number and exit
  -n, --no-banner	don't print beautiful banners
  -t			number of threads[OPTIONAL] [default : 8]
  -o			output directory [OPTIONAL] [default : current directory]
  --sample		Sample name [MANDATORY]
  --db_dir		path to centrifuge database [MANDATORY]
  --db_name		centrifuge database name [MANDATORY]

Mode 1: SPAdes assembly + contig classification
  -1			forward paired-end reads [MANDATORY]
  -2			reverse paired-end reads [MANDATORY]


Mode 2: contig classification of a fasta file (only if you already have your SPAdes or Unicycler assembly!)
  --fasta		SPAdes assembly fasta file [MANDATORY]
  -a                    Specify the assembler used: spades or unicycler. Default=spades.


Example mode 1:
plaScope.sh -1 my_reads_1.fastq.gz -2 my_reads_2.fastq.gz -o output_directory  --db_dir path/to/DB --db_name chromosome_plasmid_db --sample name_of_my_sample

Example mode 2:
plaScope.sh --fasta my_fastafile.fasta -o output_directory --db_dir path/to/DB --db_name chromosome_plasmid_db --sample name_of_my_sample -a unicycler



Github:
https://github.com/GuilhemRoyer/PlaScope

PlaScope uses a database (see this section) made of 3 files. The argument --db_dir is the path to the directory where these 3 files are located. The argument --db_name is the common part between the file names (see examples).

Databases

E. coli database

To get the E. coli database, please download the following file on Zenodo: https://doi.org/10.5281/zenodo.1311641

After extracting the tar.gz file, you will have 3 files : chromosome_plasmid_db.1.cf, chromosome_plasmid_db.2.cf and chromosome_plasmid_db.3.cf. All these files are required for PlaScope. In this case, the --db_name to use is "chromosome_plasmid_db".

Klebsiella database

To get the Klebsiella database, please download the following file on Zenodo: https://doi.org/10.5281/zenodo.1311647

After extracting the tar.gz file, you will have 3 files : Klebsiella_PlaScope.1.cf, Klebsiella_PlaScope.2.cf and Klebsiella_PlaScope.3.cf. All these files are required for PlaScope. In this case, the --db_name to use is "Klebsiella_PlaScope".

This database has not been extensively benchmarked. We only have assessed its performances by searching for plasmids and resistance genes location on a set of 12 Klebsiella pneumoniae strains from https://academic.oup.com/jac/article/73/7/1796/4966148.

Create your own database

You can also design your own database as explained on this page.

You need to prepare four files:

  • database.fna : a multifasta file of your database
>Chromosome_1
ATGGATAAGTTGCTGAACAAAAAGAT......
>Chromosome_2
GAGTGAACGGATGAAACAGAAAGACC......
>Plasmid_1
TCTCGAATGATAAAGGCTATGATGGC......
  • nodes.dmp : an artificial taxonomy (i.e. root, chromosome, plasmid)
1 | 1 |	root
2 | 1 | chromosome
3 | 1 | plasmid
  • seqid_to_taxid.map : a mapping file between the sequences and their taxonomic assignment
Chromosome_1  2
Chromosome_2  2
Plasmid_1 3
  • names.dmp : a file mapping taxonomy IDs to a name
1	|	root	|   |   |
2	|	chromosome  |   |   |
3	|	plasmide  |   |   |

Then, build your database as follow:

centrifuge-build -p 10 --conversion-table seqid_to_taxid.map --taxonomy-tree nodes.dmp --name-table names.dmp database.fna chromosome_plasmid_db

Contributors

  • Guilhem Royer (CEA-Genoscope, now at Pasteur): design, implementation, evaluation
  • David Valllenet (CEA-Genoscope): design
  • Julian Paganini (UMC Utrecht): new feature: accept unicycler assemblies