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

• Version: 1.6.3
• Added: September, 2020
• Link: https://github.com/BU-ISCIII/plasmidID/wiki

See versions of plasmidid that are available:

$ module avail plasmidid

Load one version into your environment and run it:

$ module load plasmidid/1.6.3
$ plasmidID

Note: Please use the –threads option to tell plasmidID how many CPU threads it should use or else it will automatically use all the CPUs on the system. This number should match the number of CPUs you requested in your SLURM batch allocation.

Notes from the sysadmin during installation.

$ cd /tmp
$ git clone --recursive https://github.com/BU-ISCIII/plasmidID.git -b v1.6.3
$ sudo mkdir -p /export/apps/plasmidid/1.6.3
$ sudo chown aorth /export/apps/plasmidid/1.6.3
$ python3 -m venv /export/apps/plasmidid/1.6.3
$ source /export/apps/plasmidid/1.6.3/bin/activate
# a few python modules as gleaned from the plasmidID Bioconda recipe: https://github.com/bioconda/bioconda-recipes/blob/master/recipes/plasmidid/meta.yaml
$ pip install biopython pandas scipy scikit-learn tabulate
$ cd plasmidID
$ sudo cp -r * /export/apps/plasmidid/1.6.3
$ sudo chown -R root:root /export/apps/plasmidid/1.6.3

After installation I tested the pipeline with the test data:

$ module load plasmidid/1.6.3
$ cp -r /export/apps/plasmidid/1.6.3/TEST_DATA /tmp
$ cd /tmp
$ plasmidID \
     -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 \
     -T 4