README.md

plasmidID

PlasmidID is already available to download

PlasmidID is a mapping-based, assembly-assisted plasmid identification tool that analyzes and gives graphic solution for plasmid identification.

PlasmidID is a computational pipeline implemented in BASH that maps Illumina reads over plasmid database sequences. The most covered sequences are clustered by identity to avoid redundancy and the longest are used as scaffold for plasmid reconstruction. Reads are assembled and annotated by automatic and specific annotation. All information generated from mapping, assembly, annotation and local alignment analyses is gathered and accurately represented in a circular image which allow user to determine plasmidic composition in any bacterial sample.

This image sumarizes PlasmidID pipeline, including the most important steps. For furder details, including:

• Database download
• Dependencies
• Execution
• Results interpretation
• and more, please visit: PLASMIDID WIKI

Quick usage

Example: Clone the repo:

git clone [email protected]:BU-ISCIII/plasmidID.git
cd plasmidID
git submodule init
git submodule update

Run it with the test data using docker or singularity:

Notice that the input files MUST be in your present working directory or in any folder inside it. For example, if I execute this command in /home/smonzon, my folder with the files would be in /home/smonzon/TEST_DATA.

docker run -v $PWD:$PWD -w $PWD buisciii/plasmidid plasmidID.sh \
     -1 TEST_DATA/KPN_TEST_R1.fastq.gz  \
     -2 TEST_DATA/KPN_TEST_R2.fastq.gz \
     -d TEST_DATA/plasmids_TEST_database.fasta \
     -c TEST_DATA/contigs_KPN_TEST.fasta \
     --no-trim \
     -s KPN

Or you can use Singularity instead:

singularity exec docker://buisciii/plasmidid plasmidID.sh \
     -1 TEST_DATA/KPN_TEST_R1.fastq.gz  \
     -2 TEST_DATA/KPN_TEST_R2.fastq.gz \
     -d TEST_DATA/plasmids_TEST_database.fasta \
     -c TEST_DATA/contigs_KPN_TEST.fasta \
     --no-trim \
     -s KPN

You can also build the image in your local machine cloning the repository and building it using the Singularity recipe provided:

git clone [email protected]:BU-ISCIII/plasmidID.git
cd plasmidID
git submodule init
git submodule update
singularity build plasmidid.simg Singularity
singularity exec plasmidid.simg plasmidID.sh \
     -1 TEST_DATA/KPN_TEST_R1.fastq.gz  \
     -2 TEST_DATA/KPN_TEST_R2.fastq.gz \
     -d TEST_DATA/plasmids_TEST_database.fasta \
     -c TEST_DATA/contigs_KPN_TEST.fasta \
     --no-trim \
     -s KPN

If you want to use trimming functionality you have to supply trimmomatic-directory parameter:

docker run -v $PWD:$PWD -w $PWD buisciii/plasmidid plasmidID.sh \
     -1 file_R1.fastq.gz  \
     -2 file_R2.fastq.gz \
     -d database.fasta \
     -c contigs.fasta \
     --trimmomatic-directory /scif/apps/trimmomatic/Trimmomatic-0.38 \
     -s KPN

Note: You MUST skip trimming filtering in order to use TEST_DATA as it is already filtered!