DNAINDEX(1)

💖 DNAINDEX 💖

okay bestie, so this is dnaindex from section 1 of the User Manuals — the little tool that builds the index your dna file needs before anfo(1) will even look at it. sit down, hydrate, we're doing genomics 🧬✨

---

✨ NAME ✨

dnaindex — index a dna file for use with ANFO. that's the whole job. it's giving "small but crucial". 🎀

---

🦋 SYNOPSIS 🦋

dnaindex [ option ... ]

---

💅 DESCRIPTION 💅

so dnaindex builds an index for a dna file. and here's the tea: dna files must be indexed to be useable with anfo(1). no index, no service, periodt. 🚫

but the fun part? you can have multiple indices for the same dna file. yes queen, one genome, many little index outfits. wardrobe options. 👑

---

🌸 OPTIONS 🌸

• -V, --version — prints the version number and then dips. bye. 👋
• -o file, --output file — write the output to file. file customarily ends in .idx. the default is genomename_wordsize.idx.
• -g file, --genome file — read the genome from file. heads up: this file name also gets stored in the resulting index, so it can be found automatically whenever the index is used. that's why it's best if file is just a file name without a path — don't make future-you hunt for it. 🙈
• -G dir, --genome-dir dir — add dir to the genome search path. super useful if the genome you're indexing isn't yet in the place where it'll later be used. glow-up in progress. ✨
• -d text, --description text — add text as a description to the index. this is purely informative, so write whatever cute note your heart desires. 💜
• -s size, --wordsize size — set the wordsize to size. smaller wordsize = more precision, but at the expense of higher computational investment. the default is 12, which with a stride of 8 yields a good compromise. balanced. iconic. 🎀
• -S num, --stride num — set the stride to num. only one out of num possible words of dna is actually indexed. smaller stride = more precision, but at the expense of a bigger index. the default is 8, which in conjunction with a wordsize of 12 yields a good compromise. same energy, different dial. 🦋
• -l lim, --limit lim — prevents the indexing of words that occur more often than lim times. use this to ignore repetitive seeds and save the space it would take to store them. a good default depends on the size of the genome being indexed — something like 500 works for the human genome with wordsize 12 and stride 8. 👑
• -h, --histogram — produce a histogram of word frequencies. this can be used to get an indea how the frequency distribution to select an appropriate value for --limit. (yes, "indea". we don't fix the originals around here, we respect them. 💀)
• -v, --verbose — print a progress indicator during operation. for the girlies who need to see the progress bar moving. 📈

---

🔥 NOTES 🔥

dnaindex is limited to genomes no longer than 4 gigabases due to its use of 32 bit indices. also, the index is quite large, so depending on parameters, a 64 bit platform is needed for genomes in the gigabase range. plan accordingly, bestie. 💀

if a genome contains IUPAC ambiguity codes, the affected seeds need to be expanded. and if there are many ambiguity codes in a small region, that results in an unacceptably large index. not the vibe. 😭

---

🌈 ENVIRONMENT 🌈

• ANFO_PATH — colon separated list of directories searched for genome files.

---

🎀 FILES 🎀

• /etc/popt — the system wide configuration file for popt(3). dnaindex identifies itself as "dnaindex" to popt. it knows its own name, slay.
• ~/.popt — per user configuration file for popt(3).

---

💀 BUGS 💀

None known.

(we love a flawless queen. 🫶)

---

👑 AUTHOR 👑

Udo Stenzel <udo_stenzel@eva.mpg.de>

---

⭐ SEE ALSO ⭐

anfo(1), fa2dna(1), popt(3), fasta(5)

---

ok that's the whole page, you're fully indexed and ready to go. go build that index, bestie, anfo(1) is waiting and it does NOT accept late submissions. 🧚💖

mwah 💋 — with love from the Applications section, October 2009, page DNAINDEX(1).