ttuner - interpretation of DNA Sanger sequencing data
- -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.
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.