ttuner - 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.

ttuner 3.0.6~beta                                 October 2018                                         TTUNER(1)

-h     (Help) This message

       -Q     (Quiet) Turn off status messages

       -V     (Verbose) Output more status messages

       -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

       -het   Call call hetezygotes

       -mix   Call mixed bases

       -min_ratio <ratio>
              Override the default threshold ratio of heights of

       -trim_window <size>
              Set the trimming window size for averaging quality to the specified value. The default is 10.

       -trim_threshold <qv> Set the average quality value used in trimming to

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

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

       -t <table>
              Use  specified  lookup  table.  This  option overrides the default (automatic choice of the lookup
              table) as well as the options -3700pop5, -3700pop6, -3100, and -mbace. To get  a  message  showing
              which table was used, specify -V option

       -3730  Use the built-in ABI 3730-pop7 lookup table

       -3700pop5
              Use the built-in ABI 3700-pop5 lookup table

       -3700pop6
              Use the built-in ABI 3700-pop6 lookup table

       -3100  Use the built-in ABI 3100-pop6 lookup table

       -mbace Use the built-in MegaBACE lookup table

       -c     Output SCF file(s), in the current directory

       -cd <dir>
              Output SCF file(s), in the specified directory

       -cv3   Use version 3 for output SCF file. Default is version 2.

       -o <dir>
              Output multi-fasta files of bases (tt.seq), their locations (tt.pos), quality values (tt.qual) and
              status reports (tt.status) to directory <dir>

       -p     Output .phd.1 file(s), in the current directory

       -pd <dir>
              Output .phd.1 file(s), in the specified directory

       -q     Output .qual file(s), in the current directory

       -qa <file>
              Append .qual file(s) to <file>

       -qd <dir>
              Output .qual file(s), in the specified directory

       -s     Output .seq file(s) in FASTA format, in the current directory

       -sa <file>
              Append .seq file(s) in FASTA format to <file>

       -sd <dir>
              Output .seq file(s) in FASTA format, in the specified directory

       -qr <file>
              Output a quality report that gives data for a histogram on the number of reads with quality values
              >= 20, to the specified file

       -if <file>
              Read the input sample filenames from the specified file

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

       -tab   Call heterozygotes or mixed bases and output .tab file(s) in the  current directory

       -tabd <dir>
              Call mixed bases and output .tab file(s), in the specified directory

       -tal   Output .tal file(s),in the current directory

       -tald <dir>
              Output .tal file(s),in the specified directory

       -hpr   Output a homopolymer runs file in current directory

       -hprd <dir>
              Output a homopolymer runs file(s),in the specified directory

       -d     Output .poly file(s),in the current directory

       -dd    <dir>           Output .poly file(s),in the specified directory

       -ipd <dir>
              Input the original bases and peak locations from a .phd file in the specified directory.

       ttuner - interpretation of DNA Sanger sequencing data