TTUNER(1)

💅 ttuner — like, the manual page, bestie 💅

okay so you found ttuner, which is the ttuner(1) page from the User Commands corner of the manual, and honestly? it's giving "bioinformatics but make it cute". it interprets DNA Sanger sequencing data. that's the whole vibe. let's go ✨

🌸 NAME 🌸

ttuner — interpretation of DNA Sanger sequencing data 🧬🦋

like. it takes your sequencing reads and it interprets them. that's the job. periodt.

🎀 DESCRIPTION 🎀

so this is where all the flags live, and there are a lot of them, so grab a snack 🍓. here's every single one, no skips, no cap:

✨ the flags ✨

• -h — (Help) this message. that's it, that's the flag 🫶
• -Q — (Quiet) turn off status messages. shhh 🤫
• -V — (Verbose) output more status messages. not me wanting the full play-by-play 💀
• -nocall — disable base recalling and just use the original called bases read from the input sample file. like, leave it alone, it's fine as is 🙈
• -recalln — disable adding bases to or deleting from the original called sequence. only recall Ns. nothing more, nothing less 👑
• -het — call heterozygotes
• -mix — call mixed bases
• -min_ratio <ratio> — override the default threshold ratio of heights of

okay so lowkey the original page just... stops right there. "ratio of heights of" and then nothing. no cap. i'm not gonna make something up for you bestie, that would be lying and we don't do that 💀

• -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

and this one also trails off mid-sentence in the source. iconic of it, honestly. same energy as a text that just says "we need to talk" 😭

• -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 the -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. (so if you don't say anything, you get v2, mwah 💋)
• -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. king behaviour, honestly 👑

and that's the whole thing!! no notes, slay, go sequence something 🧬💖

signing off from ttuner 3.0.6~beta, dated October 2018 — yes she's a little vintage, we love her anyway 🎀✨🦋