NAME

       oligotag - description of oligotag

       oligotag  designs  a set of oligonucleotides that can be used for tagging a set of samples
       during PCR reactions, by adding the oligonucleotides on the 5’ end of the  primers.   Many
       options allow designing a set of oligonucleotides according to specified properties.

OLIGOTAG SPECIFIC OPTIONS

       -L <filename>, --oligo-list=<filename>
              Filename  containing  a list of oligonucleotides. oligotag selects within this list
              the oligonucleotides that match the specified options.

              CAUTION:
                 Cannot be used with the -s option.

       -s ###, --oligo-size=###
              Size of oligonucleotides to be generated.

              CAUTION:
                 Cannot be used with the -L option.

              WARNING:
                 A size equal or greater than eight often leads to a very long computing time and
                 requires a large amount of memory.

       -f ###, --family-size=###
              Minimal size of the oligonucleotide family to be generated.

       -d ###, --distance=###
              Minimal Hamming distance (number of differences) between two oligonucleotides.

       -g ###, --gc-max=###
              Maximum number of G or C in the oligonucleotides.

       -a <IUPAC_PATTERN>, --accepted=<IUPAC_PATTERN>
                 Selected  oligonucleotides  are  constrained  by  the  given pattern (only IUPAC
                 symbols are allowed).

              CAUTION:
                 pattern length must have the same length as oligonucleotides.

       -r <IUPAC_PATTERN>, --rejected=<IUPAC_PATTERN>
                 Selected oligonucleotides do not match the given pattern (only IUPAC symbols are
                 allowed).

              CAUTION:
                 pattern length must have the same length as oligonucleotides.

       -p ###, --homopolymer=###
              Selected  oligonucleotides do not contain any homopolymer longer than the specified
              length.

       -P ###, --homopolymer-min=###
              Selected oligonucleotides contain at least one homopolymer longer or equal  to  the
              specified length.

       -T <seconde>, --timeout=<seconde>
              Timeout  to  identify a set of oligonucleotides of required size, as defined by the
              -f option.

COMMON OPTIONS

       -h, --help
              Shows this help message and exits.

       --DEBUG
              Sets logging in debug mode.

EXAMPLES

          Example 1:

                 > oligotag -s 5 -f 24 -d 3 -g 3 -p 2 > mytags.txt

              Searches for a family of at least 24 oligonucleotides of a length of 5 nucleotides,
              with  at  least  3  differences  among  them,  with a maximum of 3 C/G, and without
              homopolymers longer than 2. The resulting list of oligonucleotides is saved in  the
              mytags.txt file.

          Example 2:

                 >  oligotag -d 5 -L my_oligos.txt -f 10 -p 1

              Searches  for  a subset of at least 10 oligonucleotides listed in the my_oligos.txt
              file, with at least  5  differences  among  them,  and  without  homopolymers.  The
              my_oligos.txt  file must contain a set of oligonucleotides of the same length, with
              only one oligonucleotide per line.   The  resulting  list  of  oligonucleotides  is
              printed on the terminal window.

          Example 3:

                 > oligotag -s 7 -f 96 -d 3 -p 1 -r cnnnnnn > mytags.txt

              Searches for a family of at least 96 oligonucleotides of a length of 7 nucleotides,
              with at least 3 differences among them, without homopolymers, and without  a  C  in
              the first position. The resulting list is saved in the mytags.txt file.

          Example 4:

                 > oligotag -s 9 -f 24 -d 3 -a yryryryry > mytags.txt

              Searches for a family of at least 24 oligonucleotides of a length of 9 nucleotides,
              with at least 3 differences among them,  and  an  alternation  of  pyrimidines  and
              purines.   The  resulting  list  is  saved  in  the mytags.txt file. Because of the
              constraints  imposed  by  the  -a  option,  it  is  possible  to   compute   longer
              oligonucleotides in a reasonable time.

REFERENCE

       E. Coissac.  Oligotag: a program for designing sets of tags for next-generation sequencing
          of multiplexed samples. Methods Mol Biol, 888:13-31, 2012.

AUTHOR

       The OBITools Development Team - LECA

COPYRIGHT

       2019 - 2015, OBITool Development Team

 1.02 12                                   Jan 28, 2019                               OLIGOTAG(1)