trainphd - interpretation of DNA Sanger sequencing data

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

trainphd 3.0.6~beta                               October 2018                                       TRAINPHD(1)

-h     (Help) This message

       -C <consensusfile>
              Specify the name of the FASTA file which contains the consensus sequence

       -V <vector>
              Specify the name of the FASTA file which contains the vector sequence

       -P <primer>
              Specify the name of the FASTA file which contains the primer sequence

       -S <site>
              Specify the name of the FASTA file which contains the restriction site sequence

       -M <match>
              Specify the match premium     (default is 10)

       -X <mismatch>
              Specify the mismatch penalty  (default is 20)

       -G <gap_penalty >
              Specify the gap initiation or extension penalty (default is 40)

       -r <repeat_fraction>
              Specify the repeat_fraction   (default is 0.85)

       -f <max_frac_of_err>
              Specify  the  allowable  fraction  of  errors within the best alignment region. Default is 0.1. If
              actual fraction of errors exceeds this vale, the fragment will be rejected (=not used in  training
              process)

       -a <min_portion_aligned> Instructs trainphd to ignore a read if less than
              the specified portion of its bases is aligned with reference sequence (default is 0)

       -l <min_read_length>
              Instructs  trainphd  to  ignore  a  read  of  length less than specified number of basepairs (0 by
              default)

       -o <output_file>
              Specify the name of the output file. By default, the output will be made to stdout

       -t <tab_dir>
              Instructs trainphd extract alternative base calls from TAB files stored in directory  tab_dir  and
              to output these calls, together with quality value for each alternative call

       -d <dir>
              Read the input PHD files from specified directory

       -j <projectfile>
              Specify  the  name of the projectfile which comprises two columns: the full path to the FASTA file
              which contains the consensus sequence, followed by the full path to the sample file

       trainphd - interpretation of DNA Sanger sequencing data