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 and execution, please visit:
PLASMIDID WIKI

Quick usage

Example:

docker run 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 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