NAME

       train - interpretation of DNA Sanger sequencing data

DESCRIPTION

       -h     (Help) This message

       -nocall
              Disable  base  recalling and just use the original called bases read from the input
              sample file

       -recalln
              Disable adding bases to or deleting from the original called sequence. Only  recall
              Ns

       -recallndb
              Disable  adding bases to or deleting from the original called sequence. Only recall
              Ns and dye blobs

       -ladder
              Similar to -recalln, but all bases, not only Ns  will  be  recalled  from  original
              locations

       -edited_bases
              Start base recalling from the ABI's edited bases

       -het   Call heterozygous bases

       -mix   Call mixed        bases

       -min_ratio <ratio>
              Override  the  default threshold ratio of heights of the lowest peak to the highest
              peak at a given position

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

       -fe <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)

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

       -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)

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

       -p <projectfile>
              Specify  the  name  of  the projectfile which consists of two columns. Each line in
              this file contains the full path to the sample file to be processed  and  the  full
              path  to  the  FASTA file which contains the consensus sequence that should be used
              with this sample file

AUTHOR

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