---
name: "plasmidID"
section: "1"
platform: "linux"
package: "plasmidid"
version: "1.6.5+dfsg-2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/plasmidID"
---

# plasmidID(1)

plasmid identification tool

## NAME

plasmidID - plasmid identification tool

## DESCRIPTION

plasmidID is a computational pipeline tha reconstruct and annotate the most likely plasmids present in one sample

usage : ./plasmidID \<-1 R1\> \<-2 R2\> \<-d database(fasta)\> \<-s sample\_name\> \[-g group\_name\] \[options\]

-

  Mandatory input data: **-1** \| **--R1**       \<filename\>      reads corresponding to paired-end R1 (mandatory) **-2** \| **--R2**       \<filename\>      reads corresponding to paired-end R2 (mandatory) **-d** \| **--database** \<filename\>      database to map and reconstruct (mandatory) **-s** \| **--sample**   \<string\>        sample name (mandatory), less than 37 characters

-

  Optional input data: **-g** \| **--group**    \<string\>        group name (optional). If unset, samples will be gathered in NO\_GROUP group **-c** \| **--contigs**  \<filename\>      file with contigs. If supplied, plasmidID will not assembly reads **-a** \| **--annotate** \<filename\>      file with configuration file for specific annotation **-o**              \<output\_dir\>    output directory, by default is the current directory

-

  Pipeline options: **--explore**       Relaxes default parameters to find less reliable relationships within data supplied and database **--only-reconstruct**      Database supplied will not be filtered and all sequences will be used as scaffold

-

  This option does not require R1 and R2, instead a contig file can be supplied

- **-w**

  Undo winner takes it all algorithm when clustering by kmer - QUICKER MODE

-

  Trimming: **--trimmomatic-directory** Indicate directory holding trimmomatic .jar executable **--no-trim**       Reads supplied will not be quality trimmed

-

  Coverage and Clustering: **-C** \| **--coverage-cutoff**  \<int\>   minimum coverage percentage to select a plasmid as scafold (0-100), default 80 **-S** \| **--coverage-summary** \<int\>   minimum coverage percentage to include plasmids in summary image (0-100), default 90 **-f** \| **--cluster**  \<int\>   kmer identity to cluster plasmids into the same representative sequence (0 means identical) (0-1), default 0.5 **-k** \| **--kmer**     \<int\>   identity to filter plasmids from the database with kmer approach (0-1), default 0.95

-

  Contig local alignment **-i** \| **--alignment-identity** \<int\> minimum identity percentage aligned for a contig to annotate, default 90 **-l** \| **--alignment-percentage** \<int\>       minimum length percentage aligned for a contig to annotate, default 20 **-L** \| **--length-total**     \<int\>   minimum alignment length to filter blast analysis **--extend-annotation** \<int\>       look for annotation over regions with no homology found (base pairs), default 500bp

-

  Draw images: **--config-directory** \<dir\>        directory holding config files, default config\_files/ **--config-file-individual** \<file-name\> file name of the individual file used to reconstruct Additional options:

- **-M** \| **--memory**

  \<int\>   max memory allowed to use

- **-T** \| **--threads**

  \<int\>   number of threads

- **-v** \| **--version**

  version

- **-h** \| **--help**

  display usage message

example: ./plasmidID.sh **-1** ecoli\_R1.fastq.gz **-2** ecoli\_R2.fastq.gz **-d** database.fasta **-s** ECO\_553 **-G** ENTERO

-

  ./plasmidID.sh **-1** ecoli\_R1.fastq.gz **-2** ecoli\_R2.fastq.gz **-d** PacBio\_sample.fasta **-c** scaffolds.fasta **-C** 60 **-s** ECO\_60 **-G** ENTERO **--no-trim**

## SEE ALSO

The full documentation for **plasmidID** is maintained as a Texinfo manual.  If the **info** and **plasmidID** programs are properly installed at your site, the command

-

  **info plasmidID**

should give you access to the complete manual.