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

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