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.