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.

plasmidID 1.6.4                                   November 2022                                     PLASMIDID(1)