---
name: "ttuner"
section: "1"
platform: "linux"
package: "tracetuner"
version: "3.0.6~beta+dfsg-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/ttuner"
---

# ttuner(1)

interpretation of DNA Sanger sequencing data

## NAME

ttuner - interpretation of DNA Sanger sequencing data

## DESCRIPTION

- **-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.

## AUTHOR

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